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

GapMind for catabolism of small carbon sources

Aligments 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_607 Predicted L-arabinose ABC transport system, ATP-binding protein

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



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_607 Predicted
           L-arabinose ABC transport system, ATP-binding protein
          Length = 517

 Score =  447 bits (1150), Expect = e-130
 Identities = 247/499 (49%), Positives = 339/499 (67%), Gaps = 9/499 (1%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L+  G+ K F G+  L +V  +L  GEI AL+G+NGAGKSTLIK LTGV  A  G + L
Sbjct: 18  VLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRL 77

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEME----- 123
            GQA+ P +   AQ+LGI TVYQEVNL PN+SVA+N+F GR P R G+ +   ++     
Sbjct: 78  GGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYP-RCGIAQGFRIDWATLH 136

Query: 124 KRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVEL 183
           +RA +L+A  G  +DV   L+ + VA+QQ+VAI RA+ + ++VLILDEPT+SLD  EV+ 
Sbjct: 137 QRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQK 196

Query: 184 LFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243
           LF+++R+LR  G+S++FVTHFL+QVY VSDRITVLRNGS+VG     +L    L+  MLG
Sbjct: 197 LFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAMLG 256

Query: 244 RELDTHALQRAGRTLLSDKPVAAFK--NYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTE 301
           R+L   + Q A    +  +     +    G+   + P DL++R GE+VGLAGLLGSGRTE
Sbjct: 257 RDLAAASEQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSGRTE 316

Query: 302 TAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIIL 361
            A ++FG++  D G   I G+     +P  A   G+  CPE+RKTDGI+A  SVRENI L
Sbjct: 317 LARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVRENIAL 376

Query: 362 ALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRP 421
           ALQA+ G  + +SR EQ E+AER+++ LGI+T + ++PI  LSGGNQQK +L+RW+   P
Sbjct: 377 ALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMAIEP 436

Query: 422 QFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQV 481
           + LILDEPTRGIDV A  EI+  I  L   G+A+L ISSE+ E+V  A R++++RDR++V
Sbjct: 437 RLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRDRRKV 496

Query: 482 AEIPLAELSVPAIMNAIAA 500
            E+P A  S  A+ + IAA
Sbjct: 497 GELP-AGSSEDAVYDLIAA 514


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: 628
Number of extensions: 25
Number of successful extensions: 7
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: 500
Length of database: 517
Length adjustment: 34
Effective length of query: 466
Effective length of database: 483
Effective search space:   225078
Effective search space used:   225078
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.

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

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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, 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

GapMind for catabolism of small carbon sources