GapMind for catabolism of small carbon sources

 

Aligments for a candidate for btsT in Pseudomonas fluorescens FW300-N2C3

Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate AO356_25680 AO356_25680 carbon starvation protein A

Query= SwissProt::P39396
         (716 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25680 AO356_25680 carbon
           starvation protein A
          Length = 686

 Score =  977 bits (2526), Expect = 0.0
 Identities = 487/707 (68%), Positives = 579/707 (81%), Gaps = 25/707 (3%)

Query: 3   TKKIFKHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKV 62
           T ++ KH+ W  + ++GA  L+VVALRRGE I+ALWIVVA+V++YLVAYRYYSL+IA  V
Sbjct: 2   TTRLVKHLAWFAVAVLGACALSVVALRRGEPINALWIVVAAVAIYLVAYRYYSLFIANNV 61

Query: 63  MKLDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWL 122
           M+LD  RATPAV+NNDGL+YVPTN+++LFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWL
Sbjct: 62  MQLDARRATPAVLNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWL 121

Query: 123 LAGVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLAL 182
           +AGVVLAGAVQDFMVLF+S+RRNG SLG+M++EEMG +PGTIALFGCFLIMIIILAVLAL
Sbjct: 122 IAGVVLAGAVQDFMVLFLSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLAL 181

Query: 183 IVVKALAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIA 242
           IVVKALAESPWG+FTV +T+PIA+FMGIYMR+IRPGR+GE+S+IG++LL+ SI+ GG IA
Sbjct: 182 IVVKALAESPWGIFTVMATIPIAMFMGIYMRYIRPGRIGEISIIGVLLLLGSIWLGGQIA 241

Query: 243 HDPYWGPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVV 302
            DP W  A TF    IT+ LIGY FV+A+LPVWLILAPRDYL+TFLKIG IV LA+GI+V
Sbjct: 242 ADPVWAKAFTFTGIQITWMLIGYGFVAAVLPVWLILAPRDYLSTFLKIGTIVALAIGILV 301

Query: 303 LNPELKMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDA 362
             PELKMPA+TQ+ DGTGP+WKG LFPFLFITIACGAVSGFHALISSGTTPKLL NET+A
Sbjct: 302 TMPELKMPALTQFTDGTGPVWKGGLFPFLFITIACGAVSGFHALISSGTTPKLLDNETNA 361

Query: 363 RFIGYGAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMA 422
           R+IGYG MLMESFVAIMA+VAAS+IEPG+YFAMN+P A +G                   
Sbjct: 362 RYIGYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVG------------------- 402

Query: 423 QLKDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVLP 482
              DV A  A TVSSWGF I+PE +   AKDIGE +VL RAGGAPTLAVGIA + H VLP
Sbjct: 403 --GDVVA-VAQTVSSWGFAITPEALQAVAKDIGETTVLARAGGAPTLAVGIAQILHSVLP 459

Query: 483 MAD-MGFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTA 541
             + M FWYHF ILFEALFILTA+DAGTR+GRFMLQDLLG+F+P LK+T+S  A +I TA
Sbjct: 460 GENTMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPALKRTESWTANLIATA 519

Query: 542 GCVGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTV 601
           GCV LWGYLLYQGV+DPLGG+ +LWPLFGISNQMLA +AL+L TVVLIKMKR +Y+WVT+
Sbjct: 520 GCVALWGYLLYQGVIDPLGGINTLWPLFGISNQMLAGIALMLATVVLIKMKRQRYVWVTL 579

Query: 602 VPAVWLLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVVN 660
           +PA WLLICTT A  +KLF  NP + GF  +A +Y + +A G  L  A+ I  M H+V N
Sbjct: 580 LPASWLLICTTTAGLIKLFDANPAI-GFLALARKYNDALAAGQILAPAKSIEQMQHVVFN 638

Query: 661 NYTNAGLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIPE 707
            YTNA L++LFL VV+SI+FY  K  +A   + +RTDKE P+  +P+
Sbjct: 639 AYTNATLTVLFLFVVFSILFYALKVGIAAWGTKERTDKEAPFQALPD 685


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: 1505
Number of extensions: 67
Number of successful extensions: 6
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: 686
Length adjustment: 39
Effective length of query: 677
Effective length of database: 647
Effective search space:   438019
Effective search space used:   438019
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