GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Pseudomonas stutzeri RCH2

Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate GFF2613 Psest_2664 tripartite ATP-independent periplasmic transporter solute receptor, DctP family

Query= reanno::SB2B:6938088
         (339 letters)



>FitnessBrowser__psRCH2:GFF2613
          Length = 329

 Score =  337 bits (865), Expect = 2e-97
 Identities = 170/324 (52%), Positives = 224/324 (69%), Gaps = 2/324 (0%)

Query: 17  KASLLATVLGFSFGAV--AEPVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYKVSVF 74
           K   LA  L FS   +  A+PV IKF+HVVA+NTPKGQ AL FK+L E RLPG+ KV V+
Sbjct: 5   KLKALACALSFSIAGLVHADPVTIKFAHVVADNTPKGQGALLFKKLAEERLPGKVKVEVY 64

Query: 75  PNSQLFGDNNELAALLLNDVQLVAPSLSKFERYTKKLQVFDLPFLFEDMDAVDRFQQSEA 134
           PNS LFGD  E+ ALLL DV ++APSL+KFE Y K +Q++DLPFLF+D+ A DRFQ    
Sbjct: 65  PNSSLFGDGKEMEALLLGDVHMLAPSLAKFEHYAKAIQIYDLPFLFDDLAAADRFQSGPQ 124

Query: 135 GQQLLNSMSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIMPSDVIAAQFEAVGA 194
           G+ LL +M  K + GL Y HNGMKQ SAN  L  P DA G KFR+  S V+  QF+AV A
Sbjct: 125 GKALLRAMEDKNITGLAYWHNGMKQLSANKPLREPKDARGLKFRVQASAVLDEQFKAVRA 184

Query: 195 IPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVTSETFW 254
            P K  F+EV+  LQT  ++G ENTWSN  S+K +EVQ ++T S+HG++DYM++T+  FW
Sbjct: 185 NPRKMSFAEVYQGLQTGVVNGTENTWSNYESQKVHEVQPYMTASDHGLIDYMVITNTKFW 244

Query: 255 KSLPKDKREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQRQAWVNAM 314
             LP+D R  ++  M+E  A  N+ A +   + RQ I  S + E++ LTPEQR  W  AM
Sbjct: 245 NGLPEDLRGELETIMEEVTAEVNRQADDLNQQARQAIAASGKTEIIELTPEQRAQWREAM 304

Query: 315 RPVWSQFEDKIGKDLIEAAESANK 338
           +PVW +FE++IG +LIEAA++AN+
Sbjct: 305 KPVWKKFENEIGAELIEAAQAANR 328


Lambda     K      H
   0.316    0.132    0.368 

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: 300
Number of extensions: 8
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: 339
Length of database: 329
Length adjustment: 28
Effective length of query: 311
Effective length of database: 301
Effective search space:    93611
Effective search space used:    93611
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 (21.6 bits)
S2: 49 (23.5 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