BLASTP 2.2.17 [Aug-26-2007]

Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Reference for composition-based statistics:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= 0001.1963.p         (142 letters)

Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
from WGS projects 
           15,459,386 sequences; 5,307,515,862 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ref|ZP_05061391.1| helix-turn-helix domain protein [gamma proteo...   103   1e-20
ref|YP_004049974.1| hypothetical protein Sulku_2772 [Sulfuricurv...    98   4e-19
ref|ZP_08871414.1| helix-turn-helix domain-containing protein [V...    91   6e-17
ref|NP_933066.1| hypothetical protein VV0273 [Vibrio vulnificus ...    91   7e-17
ref|ZP_04753918.1| hypothetical protein AM305_11555 [Actinobacil...    88   5e-16

>ref|ZP_05061391.1| helix-turn-helix domain protein [gamma proteobacterium HTCC5015]
 gb|EDY86634.1| helix-turn-helix domain protein [gamma proteobacterium HTCC5015]
          Length = 363

 Score =  103 bits (256), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 53/134 (39%), Positives = 81/134 (60%), Gaps = 1/134 (0%)

Query: 1   MALPDDM-PEKEKEACCHRFAGALLYPKARVEADFGKRRRRVLPQELLIAKRGYGVSMQV 59
           M +P+ +  + E+E  CHRFAGA L+P+ +V   FG  R+R    E L+ K  +G+SMQ 
Sbjct: 210 MKMPESIHGDNEEERWCHRFAGAFLFPEKQVFDAFGYHRKRFYEAEFLLVKHEWGISMQA 269

Query: 60  ALRRLKDLHIIDDAGYTSMTIDIARRGWKTSEPEAMPCEHPLRFSSLVYRGLAEGLMTVS 119
           ALRRL DL I+    Y ++    + +G++ +EP+ +  E   R   LV+R LAEG++T S
Sbjct: 270 ALRRLYDLEIVGQNVYQNIFKQWSVKGYRRNEPQPLLPERSYRLKQLVFRSLAEGVITPS 329

Query: 120 RAAEFLQQPISAVE 133
           RAAE L   +  ++
Sbjct: 330 RAAELLNTSMEQID 343


>ref|YP_004049974.1| hypothetical protein Sulku_2772 [Sulfuricurvum kujiense DSM 16994]
 gb|ADR35421.1| protein of unknown function DUF955 [Sulfuricurvum kujiense DSM
           16994]
          Length = 354

 Score = 97.8 bits (242), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 48/118 (40%), Positives = 72/118 (61%)

Query: 12  KEACCHRFAGALLYPKARVEADFGKRRRRVLPQELLIAKRGYGVSMQVALRRLKDLHIID 71
           +E  CHRFAGALL PK  V+ + G  R ++  +ELL+ K+ YG+SM  ALRR  DL II 
Sbjct: 219 EEKACHRFAGALLVPKVAVQDELGTFRTKLEYRELLLLKQEYGISMSAALRRAYDLGIIK 278

Query: 72  DAGYTSMTIDIARRGWKTSEPEAMPCEHPLRFSSLVYRGLAEGLMTVSRAAEFLQQPI 129
           ++ Y  + ID ++RGW+ +EP     E    F+ L++  LAE  +  S+AA+ +   +
Sbjct: 279 ESYYKHVVIDFSQRGWRKNEPYPTKQEESHHFTQLIFHALAEEYIGESKAADLMNMSV 336


>ref|ZP_08871414.1| helix-turn-helix domain-containing protein [Verminephrobacter sp.
           At4]
          Length = 358

 Score = 90.9 bits (224), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 53/122 (43%), Positives = 69/122 (56%), Gaps = 1/122 (0%)

Query: 8   PEKEKEACCHRFAGALLYPKARVEADFGKRRRRVLPQELLIAKRGYGVSMQVALRRLKDL 67
           P   KE  C RFAGA L PKA V    G  RR V  QELL  K  +G+SM   L+R +  
Sbjct: 219 PGARKEKACDRFAGAFLAPKAAVVRSLGPVRRGVEWQELLALKHAFGLSMAGWLQRARQC 278

Query: 68  HIIDDAGYTSMTIDIARRGWKTSEP-EAMPCEHPLRFSSLVYRGLAEGLMTVSRAAEFLQ 126
            +  +A +++++ D    GW+ SEP E +P EH   F  LVYR L EG ++ S+AAE L 
Sbjct: 279 GVTTEAVHSALSQDFFSNGWRQSEPGEPVPREHSRLFGQLVYRALGEGYVSESKAAELLG 338

Query: 127 QP 128
            P
Sbjct: 339 IP 340


>ref|NP_933066.1| hypothetical protein VV0273 [Vibrio vulnificus YJ016]
 dbj|BAC93037.1| hypothetical protein [Vibrio vulnificus YJ016]
          Length = 350

 Score = 90.5 bits (223), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 49/123 (39%), Positives = 69/123 (56%), Gaps = 1/123 (0%)

Query: 11  EKEACCHRFAGALLYPKARVEADFGKRRRRVLPQELLIAKRGYGVSMQVALRRLKDLHII 70
           ++E  C+RFA A L P+  +    G+RR  V P+EL   K  YG+SM   L R  DL +I
Sbjct: 217 DEEMACNRFASAFLLPEVGLFQHLGERRSNVDPKELYFLKHEYGLSMAACLYRSADLGVI 276

Query: 71  DDAGYTSMTIDIARRGWKTSEP-EAMPCEHPLRFSSLVYRGLAEGLMTVSRAAEFLQQPI 129
            +     + I  ++ GW+  EP    P E  L F  LVYR LAEG+++ S+AAE LQ  +
Sbjct: 277 TEEKKRQIFIQFSKNGWRKQEPGNPYPQEQTLLFEQLVYRALAEGIVSESKAAELLQMSV 336

Query: 130 SAV 132
            A+
Sbjct: 337 MAL 339


>ref|ZP_04753918.1| hypothetical protein AM305_11555 [Actinobacillus minor NM305]
 gb|EER46659.1| hypothetical protein AM305_11555 [Actinobacillus minor NM305]
          Length = 356

 Score = 87.8 bits (216), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 46/122 (37%), Positives = 69/122 (56%), Gaps = 2/122 (1%)

Query: 11  EKEACCHRFAGALLYPKARVEADFGKRRRRVLPQELLIAKRGYGVSMQVALRRLKDLHII 70
           ++E  CHRFA A L PK     + G++R  +   EL   K+ +G+SMQ  L R KDL I+
Sbjct: 218 DEEKACHRFASAFLLPKDSAFNELGEKRSDISIYELKALKQEFGLSMQACLYRAKDLGIV 277

Query: 71  DDAGYTSMTIDIARRGWKTSEP--EAMPCEHPLRFSSLVYRGLAEGLMTVSRAAEFLQQP 128
            +  Y    I  +  GW+  EP  + +  E  L F  LV+R L+E ++T S+AAE L+ P
Sbjct: 278 SEYWYKQKCIQFSSLGWRKKEPYEDIVYQEQTLLFKQLVHRALSEDIITESKAAELLKMP 337

Query: 129 IS 130
           ++
Sbjct: 338 LT 339