Alignments for a candidate for btsT in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for btsT in Azospirillum brasilense Sp245

Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate AZOBR_RS22555 AZOBR_RS22555 carbon starvation protein CstA

Query= SwissProt::P39396
         (716 letters)



>FitnessBrowser__azobra:AZOBR_RS22555
          Length = 603

 Score =  429 bits (1102), Expect = e-124
 Identities = 246/667 (36%), Positives = 369/667 (55%), Gaps = 76/667 (11%)

Query: 36  ALWIVVASVSVYLVAYRYYSLYIAQKVMKLDPTRATPAVINNDGLNYVPTNRYVLFGHHF 95
           AL  V+A++ +  + YR+Y ++  +KV++ D +  TP+ I  DG NYVPT ++V  G HF
Sbjct: 4   ALTFVIATLCILALCYRFYGVFFVRKVLRADDSEVTPSHILADGRNYVPTKKWVNAGQHF 63

Query: 96  AAIAGAGPLVGPVLAAQMGYLPGTLWLLAGVVLAGAVQDFMVLFISSRRNGASLGEMIKE 155
           AAIA AGPLVGPVLAAQ GYLP  LWLL G V+ GAV D +VLF S +  G SL E+ K 
Sbjct: 64  AAIAAAGPLVGPVLAAQFGYLPSFLWLLIGCVIGGAVHDTVVLFASMKHKGQSLSEVAKA 123

Query: 156 EMGPVPGTIALFGCFLIMIIILAVLALIVVKALAESPWGVFTVCSTVPIALFMGIYMRFI 215
           E+GPV G         I+ I +A L+++VV AL  + WG F V  T+PIA+ +G+Y +  
Sbjct: 124 ELGPVAGWCTGLAMLFIITITMAGLSMVVVHALERNAWGAFAVFMTIPIAVALGLYEKI- 182

Query: 216 RPGRVGEVSVIGIVLLVASIYFGGVIAHDPYWGPALTFKDTTITFALIGYAFVSALLPVW 275
             G     + +GI  + AS+ F G        G  LT    T+   L  YAF +  LPVW
Sbjct: 183 -TGSSKGATQVGIAAIAASV-FAGPYIQGTVLGSWLTLHAETVALILPIYAFFATALPVW 240

Query: 276 LILAPRDYLATFLKIGVIVGLALGIVVLNPELKMPAMTQYIDGTGPLWKGALFPFLFITI 335
           ++L PR YL++F+KIGV   L +G+V +NPE++ PA+T +I G GP+  G ++PF+ ITI
Sbjct: 241 MLLTPRGYLSSFMKIGVFGALVVGVVFINPEIRFPALTDFIHGGGPVLAGPVWPFISITI 300

Query: 336 ACGAVSGFHALISSGTTPKLLANETDARFIGYGAMLMESFVAIMALVAASIIEPGLYFAM 395
           ACGA+SGFHA I SGTTPKL+   +D R + +G ML E  V +MAL+AA+ + P  YFA+
Sbjct: 301 ACGAISGFHAFIGSGTTPKLIDKWSDIRTVAFGGMLAECVVGVMALIAATSLHPADYFAI 360

Query: 396 NTPPAGLGITMPNLHEMGGENAPIIMAQLKDVTAHAAATVSSWGFVISPEQILQTAKDIG 455
           N+ PA                   +  Q+ D+                     + +++IG
Sbjct: 361 NSSPAAF---------------QALNMQVVDLP--------------------RLSQEIG 385

Query: 456 EPSVLNRAGGAPTLAVGIAHVFHKVLPMADM-GFWYHFGILFEALFILTALDAGTRSGRF 514
              +  R GGA TLAVG+  +F ++     +  +++ F ++FEA+FILTA+D+GTR  R+
Sbjct: 386 -LDLYGRTGGAVTLAVGMTEIFTRIPWFGTLASYFFQFVVMFEAVFILTAVDSGTRVARY 444

Query: 515 MLQDLLGNFIPFLKKTDSLVAGIIGTAGCVGLWGYLLYQGVVDPLGGVKSLWPLFGISNQ 574
           ++QDL G+    LK+ D +   I  +      WGYLL        G + S+W LFG+SNQ
Sbjct: 445 LIQDLGGDLYAPLKRLDWVPGSIAASVLACVAWGYLLTS------GDINSVWALFGVSNQ 498

Query: 575 MLAAVALVLGTVVLIKM-KRTQYIWVTVVPAVWLLICTTWALGLKLFSTNPQMEGFFYMA 633
           ++A+V L++G  +++++ ++  Y+   +VP  +L +   +A             G++ + 
Sbjct: 499 LMASVGLIIGATIILRLGQKRVYMLTCLVPLAYLFVTVNYA-------------GYWMIT 545

Query: 634 SQYKEKIANGTDLTAQQIANMNHIVVNNYTNAGLSILFLIVVYSIIFYGFKTWLAVRNSD 693
           + Y   +A G                 N  NAG+SI+ L + + I+    K W  +    
Sbjct: 546 NVYLNPLAKG----------------YNVFNAGISIIMLSLGFVILIAALKKWKELLRIR 589

Query: 694 KRTDKET 700
           K    ET
Sbjct: 590 KDNMPET 596


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: 1150
Number of extensions: 62
Number of successful extensions: 6
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: 716
Length of database: 603
Length adjustment: 38
Effective length of query: 678
Effective length of database: 565
Effective search space:   383070
Effective search space used:   383070
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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Candidates (tab-delimited)
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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources