GapMind for catabolism of small carbon sources

 

Aligments for a candidate for btsT in Pseudomonas fluorescens GW456-L13

Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate PfGW456L13_1444 Carbon starvation protein A

Query= SwissProt::P39396
         (716 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1444 Carbon
           starvation protein A
          Length = 688

 Score =  980 bits (2533), Expect = 0.0
 Identities = 485/702 (69%), Positives = 580/702 (82%), Gaps = 25/702 (3%)

Query: 8   KHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKVMKLDP 67
           +H+PW++L I+GA  L VVALRRGE I+ALWIVVA+V++YLVAYRYYSL+IA  VM+LD 
Sbjct: 9   RHLPWLVLAIVGACALGVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANNVMQLDA 68

Query: 68  TRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLLAGVV 127
            RATPAV+NNDGL+YVPTN+++LFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWL+AGVV
Sbjct: 69  RRATPAVLNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAGVV 128

Query: 128 LAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLALIVVKA 187
           LAGAVQDFMVLF+S+RRNG SLG+M++EEMG +PGTIALFGCFLIMIIILAVLALIVVKA
Sbjct: 129 LAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLALIVVKA 188

Query: 188 LAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIAHDPYW 247
           LAESPWG+FTV +T+PIA+FMGIYMR+IRPGR+GE+SVIG++LL+ SI+ GG IA DP W
Sbjct: 189 LAESPWGIFTVMATIPIAMFMGIYMRYIRPGRIGEISVIGVLLLLGSIWLGGQIAADPVW 248

Query: 248 GPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVVLNPEL 307
             A +F    IT+ LIGY FV+A+LPVWLILAPRDYL+TFLKIG IV LA+GI+V  PEL
Sbjct: 249 AKAFSFTGIQITWMLIGYGFVAAVLPVWLILAPRDYLSTFLKIGTIVALAIGILVTMPEL 308

Query: 308 KMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDARFIGY 367
           KMPA+TQ++DGTGP+WKG LFPFLFITIACGAVSGFHALISSGTTPKLL NET+AR+IGY
Sbjct: 309 KMPALTQFVDGTGPVWKGGLFPFLFITIACGAVSGFHALISSGTTPKLLDNETNARYIGY 368

Query: 368 GAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMAQLKDV 427
           G MLMESFVAIMA+VAAS+IEPG+YFAMN+P A +G                      DV
Sbjct: 369 GGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAVVG---------------------GDV 407

Query: 428 TAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVLPMAD-M 486
            A A A VS+WGF I+PE +   A DIGE ++L RAGGAPTLAVGIA + H VLP  + M
Sbjct: 408 VAVATA-VSNWGFAITPEALQAVAHDIGETTILARAGGAPTLAVGIAQILHSVLPGENTM 466

Query: 487 GFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTAGCVGL 546
            FWYHF ILFEALFILTA+DAGTR+GRFMLQDLLG+F+P LK+T+S  A +I TAGCV +
Sbjct: 467 AFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAM 526

Query: 547 WGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTVVPAVW 606
           WG+LLYQGV+DPLGG+ +LWPLFGISNQMLA +AL+LGTVVLIKMKR +Y+WVT++PAVW
Sbjct: 527 WGWLLYQGVIDPLGGINTLWPLFGISNQMLAGIALMLGTVVLIKMKRQRYVWVTMLPAVW 586

Query: 607 LLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVVNNYTNA 665
           LLICTT A  +KLF  NP + GF  +A +Y + +ANG  L  A+ I  M H++ N YTNA
Sbjct: 587 LLICTTTAGFIKLFDANPAI-GFLSLAKKYSDALANGQILAPAKDITQMQHVIFNAYTNA 645

Query: 666 GLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIPE 707
            L+ LFL VV+SI+FY  K  +A     +RTDKE+P+  +P+
Sbjct: 646 TLTALFLFVVFSILFYALKVGIAAWGKKERTDKESPFQALPD 687


Lambda     K      H
   0.327    0.142    0.440 

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: 1549
Number of extensions: 73
Number of successful extensions: 7
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: 716
Length of database: 688
Length adjustment: 39
Effective length of query: 677
Effective length of database: 649
Effective search space:   439373
Effective search space used:   439373
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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