GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pedobacter sp. GW460-11-11-14-LB5

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Pedo557:CA265_RS10520
          Length = 568

 Score =  105 bits (262), Expect = 2e-27
 Identities = 73/241 (30%), Positives = 130/241 (53%), Gaps = 21/241 (8%)

Query: 2   AQEPILTARGLVKRY-------GRVT----ALDRADFDLYPGEILAVIGDNGAGKSSMIK 50
           AQEP+L  + L   Y       G+ T    A+D+ +F+++PGE L ++G++G GK+++ +
Sbjct: 305 AQEPLLQIKNLCTWYPIHNGLFGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGR 364

Query: 51  AISGAVTPDEGEIRLEGKPIQF--RSPMEARQAGIETVYQNLALSPALSIADNMFLGREI 108
            I   + P  GEI   G+ I    ++ +   +  I+ ++Q+    P  S+   + +G+ I
Sbjct: 365 TILRLIQPTSGEIIFNGENITHIGKTALRKLRKDIQIIFQD----PYASLNPKLSIGQSI 420

Query: 109 RKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAF 168
            +P  + K +R  + +  +++    L ++GL   ++ N+     SGGQRQ V +ARA A 
Sbjct: 421 LEPLQVHKLYR--NDSERKQKVLELLDKVGLKE-EHFNRYPHEFSGGQRQRVVIARALAL 477

Query: 169 GSKVVIMDEPTAALGVKESRRVLELILDVRRR-GLPIVLISHNMPHVFEVADRIHIHRLG 227
             K +I DE  +AL V    +VL LI D++   GL  + ISH++  V  ++DRI +   G
Sbjct: 478 QPKFIICDESVSALDVSVQAQVLNLIKDLQSEFGLTYIFISHDLAVVKHISDRILVMNKG 537

Query: 228 R 228
           +
Sbjct: 538 K 538



 Score = 76.6 bits (187), Expect = 1e-18
 Identities = 59/212 (27%), Positives = 109/212 (51%), Gaps = 16/212 (7%)

Query: 21  ALDRADFDLYPGEILAVIGDNGAGKS----SMIKAISGAVTPDEGEIRLEGKPIQFRSPM 76
           A+ +  F +  G +L ++G++G+GKS    S+++          GEI  E   +   S  
Sbjct: 22  AVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGEIDFEDISLLNLSSN 81

Query: 77  EARQA---GIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAK 133
           E RQ     I  ++Q     P  S+      G ++ +  ++    R +D+A  +K   A 
Sbjct: 82  EIRQIRGNQISMIFQ----EPMTSLNPVFTCGYQVAEAIML---HRKVDQAEAKKHTIAL 134

Query: 134 LSELGLMTIQNINQAV-ETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLE 192
            +E+ L   + I ++    +SGGQ+Q V +A A +   K++I DEPT AL V   + +L+
Sbjct: 135 FNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQKTILQ 194

Query: 193 LILDVRR-RGLPIVLISHNMPHVFEVADRIHI 223
           L+L +++ R + ++ ISH++  V E+AD + +
Sbjct: 195 LLLKLKQERNMAMIFISHDLGVVNEIADEVAV 226


Lambda     K      H
   0.321    0.136    0.383 

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: 285
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 260
Length of database: 568
Length adjustment: 30
Effective length of query: 230
Effective length of database: 538
Effective search space:   123740
Effective search space used:   123740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory