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_RS18105 AZOBR_RS18105 carbon starvation protein A

Query= SwissProt::P39396
         (716 letters)



>FitnessBrowser__azobra:AZOBR_RS18105
          Length = 688

 Score =  870 bits (2247), Expect = 0.0
 Identities = 431/699 (61%), Positives = 534/699 (76%), Gaps = 25/699 (3%)

Query: 5   KIFKHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKVMK 64
           +I  H PW++L ++GAF L  VAL RGE I+ALW+VVA+V  YLV+YRYYSL+IA +VM+
Sbjct: 3   RILNHAPWLVLAVLGAFALGTVALARGETINALWLVVAAVCTYLVSYRYYSLFIATRVMR 62

Query: 65  LDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLLA 124
           LDP R TPA+ +NDGL+YVPTN+YVLFGHHFAAIAGAGPLVGPVLAAQMGYLPG LW+LA
Sbjct: 63  LDPARPTPAMRHNDGLDYVPTNQYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGMLWILA 122

Query: 125 GVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLALIV 184
           GVV+AGAVQDFM+LF+S RR+G SLGE+IK E+G +PG IALFG F+IM+IILAVLAL+V
Sbjct: 123 GVVVAGAVQDFMILFVSMRRDGRSLGELIKAELGDIPGVIALFGTFMIMVIILAVLALVV 182

Query: 185 VKALAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIAHD 244
           VKAL  SPWG FTV +TVPIALFMGIYMRF+RPGR+GE+S+IG  LL+A+I  GG +A  
Sbjct: 183 VKALTNSPWGFFTVAATVPIALFMGIYMRFLRPGRIGEISIIGFFLLIAAILLGGQVAQS 242

Query: 245 PYWGPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVVLN 304
             W P  T     IT+ LIGY FV+++LPVWL+LAPRDYL+TFLK+G IV LAL I+++ 
Sbjct: 243 ETWAPVFTLTGVQITWILIGYGFVASVLPVWLLLAPRDYLSTFLKVGTIVMLALCILLVA 302

Query: 305 PELKMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDARF 364
           P +KMP++T++IDGTGP+W G+LFPFLFITIACGAVSGFHALISSGTTPK++ NE   RF
Sbjct: 303 PPMKMPSVTRFIDGTGPVWSGSLFPFLFITIACGAVSGFHALISSGTTPKMVENELHTRF 362

Query: 365 IGYGAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMAQL 424
           IGYG ML ESFVA+MALVAAS IEPG+YFAMN+PPA LG T  +                
Sbjct: 363 IGYGGMLTESFVAVMALVAASCIEPGIYFAMNSPPALLGTTAES---------------- 406

Query: 425 KDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVL-PM 483
                 AA  +++WGFVI+PE I QTA+D+GE S+L+RAGGAPTLAVG+A +F ++    
Sbjct: 407 ------AAQVINNWGFVITPEMITQTAQDVGEVSILSRAGGAPTLAVGMAQIFSELFGGK 460

Query: 484 ADMGFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTAGC 543
             M FWYHF ILFEALFILTA+DAGTR+GRFMLQDLLG F   L++T S    +I T  C
Sbjct: 461 GMMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGVFFKPLQRTASWAGNLIATGLC 520

Query: 544 VGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTVVP 603
           V  WGY+LYQGVVDPLGG+ + WPLFGISNQMLA +AL+L TVVL +MKR +Y WVT+VP
Sbjct: 521 VAAWGYILYQGVVDPLGGINTFWPLFGISNQMLAGIALILATVVLFRMKRERYAWVTMVP 580

Query: 604 AVWLLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVVNNY 662
           A WLLICT  A   K+F +NP + GF   A ++      G  L  A  +  M  ++ N+Y
Sbjct: 581 AAWLLICTLTAGVQKVFHSNPAI-GFLAHAERFSTAANEGRLLAPATSMEQMRQVIFNDY 639

Query: 663 TNAGLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETP 701
            +A L+ LF++VV +++ +G  + L    SD+ T +E P
Sbjct: 640 LDAALASLFVLVVLAVLVFGVLSCLKALRSDRPTTREIP 678


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: 1449
Number of extensions: 69
Number of successful extensions: 4
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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