Alignments for a candidate for ytfR in Stutzerimonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Stutzerimonas stutzeri A1501

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_011914604.1 PST_RS17845 ABC transporter ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>NCBI__GCF_000013785.1:WP_011914604.1
          Length = 525

 Score =  223 bits (567), Expect = 2e-62
 Identities = 158/492 (32%), Positives = 246/492 (50%), Gaps = 24/492 (4%)

Query: 10  LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLE 69
           ++  G+SK F G  AL   DF+ R GE+ ALLGENGAGKS+L+    G+Y  + G++ + 
Sbjct: 7   IQLSGVSKSFDGFMALSQADFTARWGEVHALLGENGAGKSSLMNIAAGLYAPESGSLLIN 66

Query: 70  GQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNL------------FIGREPKRFGLL 117
             A+       A +  IG V+Q   L+   +VA+N+            F G   +R   L
Sbjct: 67  DNAVRLSGPRDASRYHIGMVHQHFKLVKPFTVAENIQLALPEGPGNHAFSGSHRQRLAAL 126

Query: 118 RRKEMEKRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLD 177
                E+R ++  A  GFS+D R+     SVA QQ V I + +   A++LILDEPTA L 
Sbjct: 127 -----EQRISDKAAELGFSIDPRKITESLSVAEQQRVEILKVLLAGARILILDEPTAVLT 181

Query: 178 TQEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIEL 237
             E E L + +R    +G ++I VTH +  V + +DR+TV+R G  +   +   +   EL
Sbjct: 182 DGEAERLLETVRAFARQGAAVILVTHKMSDVKRFADRVTVMRGGRTIQTLDPQTVSVPEL 241

Query: 238 VKMMLGRELDTHALQRA--GRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLL 295
           V++ +G        Q A  G   L  + + +    G +G +   +L +R GEI G+AG+ 
Sbjct: 242 VRLTVGESAPASEYQPAIPGEVRLQVRDLRS-TGAGGQGVLNGVNLSLRAGEIYGIAGVG 300

Query: 296 GSGRTETAEVIFGIKPADSGTALIKGKPQNLR-SPHQASVLGIGFCPEDRKTDGIIAAAS 354
           G+G++E A V+ G+     GT  + G     R S  Q   L I   P DR    +    S
Sbjct: 301 GNGQSELANVLMGLPEPCDGTLELTGFGDLRRASAEQRRELRIAAIPADRYGAALAGELS 360

Query: 355 VRENIILAL--QAQRGWLRPISRKEQQEIAERFIRQLGIR-TPSTEQPIEFLSGGNQQKV 411
           V EN  +      + G    + RK  +  A   +    ++   S +Q    LSGGN QK+
Sbjct: 361 VAENFGVGQVHSGRYGSFFRLRRKRLEAEAAEAVAGFDVQGVRSLKQKAALLSGGNAQKL 420

Query: 412 LLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADR 471
           +++R     P  +++  P+RG+DV A A +   +      G A+LVIS +L+E++  ADR
Sbjct: 421 VIAREFSRDPLLVLVHSPSRGLDVRATAAVHARLRAAREAGAAVLVISEDLDEVLALADR 480

Query: 472 VIIMRDRKQVAE 483
           + +M   + VAE
Sbjct: 481 IGVMSGGRIVAE 492



 Score = 78.2 bits (191), Expect = 7e-19
 Identities = 61/221 (27%), Positives = 102/221 (46%), Gaps = 9/221 (4%)

Query: 280 DLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGF 339
           D   R GE+  L G  G+G++    +  G+   +SG+ LI      L  P  AS   IG 
Sbjct: 26  DFTARWGEVHALLGENGAGKSSLMNIAAGLYAPESGSLLINDNAVRLSGPRDASRYHIGM 85

Query: 340 CPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIA--ERFIRQLGIRTPSTE 397
             +  K   ++   +V ENI LAL    G     S   +Q +A  E+ I         + 
Sbjct: 86  VHQHFK---LVKPFTVAENIQLALPEGPG-NHAFSGSHRQRLAALEQRISDKAAELGFSI 141

Query: 398 QP---IEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLA 454
            P    E LS   QQ+V + + LL   + LILDEPT  +  G    ++  +      G A
Sbjct: 142 DPRKITESLSVAEQQRVEILKVLLAGARILILDEPTAVLTDGEAERLLETVRAFARQGAA 201

Query: 455 LLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIM 495
           +++++ ++ ++  +ADRV +MR  + +  +    +SVP ++
Sbjct: 202 VILVTHKMSDVKRFADRVTVMRGGRTIQTLDPQTVSVPELV 242


Lambda     K      H
   0.321    0.138    0.391 

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: 580
Number of extensions: 32
Number of successful extensions: 8
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: 500
Length of database: 525
Length adjustment: 35
Effective length of query: 465
Effective length of database: 490
Effective search space:   227850
Effective search space used:   227850
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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 2024 update 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