Here is an example of an excellent BLAST match (E-value 0) between gene 0189 in C. pneumoniae and gene 131 in C. trachomatis.

Query:  CPn0189                                                     Score    E-
                                                                   (bits)  Value

Aligned with CT131 hypothetical protein                             1240  0.0

Query: 1    MKRRSWLKILGICLGSSIVLGFLIFLPQLLSTESRKYLVFSLIHKESGLSCSAEELKISW 60
            MKR  W KI G  L   + L  L  LP+  S+ES KYL  S+++KE+GL    E+L +SW
Sbjct: 1    MKRSPWYKIFGYYLLVGVPLALLALLPKFFSSESGKYLFLSVLNKETGLQFEIEQLHLSW 60

Query: 61   FGRQTARKIKLTG-EAKDEVFSAEKFELDGSLLRLLIYKKPKGITLSGWSLKINEPASID 119
            FG QTA+KI++ G ++  E+F+AEK  + GSL RLL+Y+ PK +TL+GWSL+I+E  S++
Sbjct: 61   FGSQTAKKIRIRGIDSDSEIFAAEKIIVKGSLPRLLLYRFPKALTLTGWSLQIDESLSMN 120

                                     .
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                                     .
                                     etc.
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                                     .

Query: 1019 ICKRLDALIDRRIRLALWGKTDIAHDRLFMTLGIDPEVIKKYFHNTSLKTKNFFLIKIRG 1078
            ICKR DALID RIRLALWGKTDI  +RL MTLGIDPE+IKK F NT LKTKNFFLIKIRG
Sbjct: 1020 ICKRFDALIDGRIRLALWGKTDIVRERLAMTLGIDPELIKKLFRNTMLKTKNFFLIKIRG 1079

Query: 1079 SISSPEVDWSSAYARIALLKSYSLGNPFSSLADKLFSSLGDSTPPPTVHPFPWEKS 1134
             ISSPE+DWSSAYARIALLKSY++  P +SLADKLFSSLG+ TP  TV P PWE S
Sbjct: 1080 PISSPEIDWSSAYARIALLKSYTIAGPLNSLADKLFSSLGEPTPTQTVSPLPWEVS 1135

A marginal E-value of 4e-05 is illustrated by the BLAST alignment between gene 0211 in C. pneumoniae and gene 228 in C. trachomatis. BLAST queries yielding marginal E-values were not reanalyzed using Psi-BLAST in this study.

Query= CPn0211 
                                                                   Score     E
                                                                   (bits)  Value

Aligned with CT228 hypothetical protein (acidic)                     39   4e-05

Query: 5  DISNVQASSIQSALLHKTSDQIQQKRCFKQSTFVILAVSLVIIGSLFLLAGVAILTVFSH 64
          D S++   +     +  TS   +   C K     IL ++L I+G+L ++AGV  L + + 
Sbjct: 8  DASSLPLPTASCVEIKSTSSSTKGNTCSK-----ILDIALAIVGALVVVAGVLALVLCAS 62

Query: 65 GVLSLVFGVLGIVLGLLLLAGGVGLLV 91
           V+    G+  +++G   +  G+  L+
Sbjct: 63 NVIFTAIGIAALIIGSACVGAGISRLM 89