GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1444
          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:

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