GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Herbaspirillum seropedicae SmR1

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate HSERO_RS19990 HSERO_RS19990 acetyl-CoA acetyltransferase

Query= uniprot:B2SYZ2
         (400 letters)



>FitnessBrowser__HerbieS:HSERO_RS19990
          Length = 400

 Score =  647 bits (1669), Expect = 0.0
 Identities = 321/400 (80%), Positives = 360/400 (90%)

Query: 1   MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60
           M D FICDAIRTPIGRYGGALKDVRADDLGAVP++AL+ERNP VDW+ VDDVIYGCANQA
Sbjct: 1   MKDVFICDAIRTPIGRYGGALKDVRADDLGAVPLRALMERNPQVDWKAVDDVIYGCANQA 60

Query: 61  GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120
           GEDNRNVARMS LLAGLP E PGSTINRLCGSGMDA+GTAARAIK+GE +LMIAGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPQEVPGSTINRLCGSGMDALGTAARAIKSGETQLMIAGGVESM 120

Query: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180
           TRAPFVMGKA SAF+RQA I DTTIGWRF+N LMK++YGVD+MPETAENVA +F VSRAD
Sbjct: 121 TRAPFVMGKADSAFSRQAAIQDTTIGWRFVNALMKQKYGVDAMPETAENVAVDFKVSRAD 180

Query: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPRETSLESLGKLKGV 240
           QD FA+ SQ KAA AQ +GTLAQEIV V I QKKGDP+    DEHPR TS+E+L +LKGV
Sbjct: 181 QDQFAVRSQAKAAAAQANGTLAQEIVPVVIPQKKGDPITVTQDEHPRATSMEALARLKGV 240

Query: 241 VRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPAP 300
           V+PDGSVTAGNASGVNDGACALLLA+ +A ++Y L+ RAR++GMATAGV PRIMG+GPAP
Sbjct: 241 VKPDGSVTAGNASGVNDGACALLLASAEAVEKYQLKPRARILGMATAGVAPRIMGMGPAP 300

Query: 301 ATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLGA 360
           A++K+L QLGMT++Q+DVIELNEAFASQGLAVLR LG+ DDD RVNPNGGAIALGHPLG 
Sbjct: 301 ASKKVLAQLGMTIDQMDVIELNEAFASQGLAVLRELGVADDDARVNPNGGAIALGHPLGM 360

Query: 361 SGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400
           SGARL+TTA YQLERT GR+ALCTMCIGVGQGIA+VIER+
Sbjct: 361 SGARLVTTATYQLERTGGRYALCTMCIGVGQGIAMVIERV 400


Lambda     K      H
   0.318    0.135    0.386 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 598
Number of extensions: 13
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate HSERO_RS19990 HSERO_RS19990 (acetyl-CoA acetyltransferase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.5619.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5619.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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