Alignments for a candidate for ytfR in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Acidovorax sp. GW101-3H11

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_609
          Length = 505

 Score =  325 bits (832), Expect = 3e-93
 Identities = 196/503 (38%), Positives = 295/503 (58%), Gaps = 16/503 (3%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVY-HAD-RGTI 66
           +L    + K FPGV AL+ V+  ++ GEI A++GENGAGKSTL+K L+GVY H    G I
Sbjct: 2   LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61

Query: 67  WLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRA 126
             +GQ         ++ LGI  ++QE+ L+P +S+A+N+F+G E  R G++       RA
Sbjct: 62  LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETARHGVIDWMAAHSRA 121

Query: 127 TELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFD 186
             L+   G       P+ +  V  QQ+V I +A+    ++LILDEPTASL+  + + L D
Sbjct: 122 QALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQALLD 181

Query: 187 LMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIE--LVKMMLGR 244
           L+ +L+ +G++ I ++H L+++ +V+D ITVLR+GS V   +  E P  E  +++ M+GR
Sbjct: 182 LLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVIQAMVGR 241

Query: 245 ELDTHALQRAGRTLLSDKPVAAFKNY-------GKKGTIAPFDLEVRPGEIVGLAGLLGS 297
           E+     QR  +     + V   +N+         +  +   DL VR GEIVG+AGL+G+
Sbjct: 242 EMSDRYPQRQPQV---GEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGA 298

Query: 298 GRTETAEVIFGIKPAD--SGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASV 355
           GRTE A  IFG       SG   + G+P ++ +  +A   G+ +  EDRK +G++    +
Sbjct: 299 GRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNEDI 358

Query: 356 RENIILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSR 415
           + N  LA      +   I   ++  +A+ +  +L IR    +Q    LSGGNQQKV+LS+
Sbjct: 359 QFNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKVVLSK 418

Query: 416 WLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM 475
           WL T P+ LILDEPTRGIDVGA  EI  LI  L A+G  ++VISSE+ EL+G  DR+ +M
Sbjct: 419 WLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIYVM 478

Query: 476 RDRKQVAEIPLAELSVPAIMNAI 498
            + + VAE+P +E S   IM AI
Sbjct: 479 NEGRFVAEMPTSEASQEKIMRAI 501



 Score = 70.9 bits (172), Expect = 1e-16
 Identities = 63/230 (27%), Positives = 106/230 (46%), Gaps = 16/230 (6%)

Query: 25  LDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADR--GTIWLEGQAISPKNTAHAQ 82
           L  +D ++RRGEI+ + G  GAG++ L  ++ G     R  G + L GQ I       A 
Sbjct: 277 LKGIDLNVRRGEIVGIAGLMGAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAV 336

Query: 83  QLGIGTVYQEVN---LLPNMSVADNLFIGREPK-RFGLLRRKEMEKRATELMASYGFSLD 138
             G+  V ++     L+ N  +  N  +   P   F  +     E R  +    Y   L 
Sbjct: 337 SHGLAYVTEDRKGNGLVLNEDIQFNTSLANLPGVSFASVIDSGQEHRVAQ---DYREKLR 393

Query: 139 VR------EPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLR 192
           +R      + LN  S   QQ V + + +  S +VLILDEPT  +D      ++ L+ QL 
Sbjct: 394 IRCSGVDQKTLN-LSGGNQQKVVLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLA 452

Query: 193 DRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMML 242
             G  +I ++  + ++  ++DRI V+  G FV    T E  Q ++++ ++
Sbjct: 453 AEGKCVIVISSEMPELLGITDRIYVMNEGRFVAEMPTSEASQEKIMRAIV 502


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: 574
Number of extensions: 30
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: 505
Length adjustment: 34
Effective length of query: 466
Effective length of database: 471
Effective search space:   219486
Effective search space used:   219486
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 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