Alignments for a candidate for ytfR in Vagococcus penaei CD276

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Vagococcus penaei CD276

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_077275992.1 BW732_RS06505 ABC transporter ATP-binding protein

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



>NCBI__GCF_001998885.1:WP_077275992.1
          Length = 521

 Score =  276 bits (707), Expect = 1e-78
 Identities = 164/491 (33%), Positives = 268/491 (54%), Gaps = 6/491 (1%)

Query: 5   QHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRG 64
           Q   ++    ++K F   KA DN++  +++GEI ALLGENGAGKSTL+  L+G+     G
Sbjct: 3   QENYVIEMRNITKQFGEFKANDNINLQIKKGEIHALLGENGAGKSTLMNVLSGLLQPTSG 62

Query: 65  TIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEK 124
            I+++G+ ++      A + GIG V+Q   L+   +V +N+ +G EP   G+L +    K
Sbjct: 63  QIYMDGKPVNFSGPTDASKRGIGMVHQHFMLVDAFTVTENIILGDEPVDKGMLDKAVAAK 122

Query: 125 RATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELL 184
               +   YG  +     ++  SV MQQ V I + +   A +LI DEPTA L  QE++ L
Sbjct: 123 EIERISKQYGMEVVPSALISDISVGMQQRVEILKTLYRGANILIFDEPTAVLTPQEIDEL 182

Query: 185 FDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGR 244
              M++L   G S+I +TH LD++ +V+DR TV+R G  +      ++   EL  +M+GR
Sbjct: 183 ILTMKELVKEGKSIIIITHKLDEIKKVADRCTVIRRGKSIDTVTVKDVSSQELADLMVGR 242

Query: 245 ELDTHALQR---AGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTE 301
            +     +R       +LS   +   ++ G    +    L+VR GE+VG+AG+ G+G+TE
Sbjct: 243 SVSFKTEKRPPKPNEAILSINDLYVKESRG-LDAVKGLSLDVRGGEVVGIAGIDGNGQTE 301

Query: 302 TAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIIL 361
             + I G++  + GT  IKGK    + P Q + +GIG  PEDR   G++   S+ +NI L
Sbjct: 302 LIQAITGLRKVEKGTVTIKGKDVTNQRPRQITEVGIGHVPEDRHKYGLVLEMSLADNIAL 361

Query: 362 ALQAQRGWLRP--ISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLT 419
                  + +   +++K   + A + I +  +RT     P   LSGGNQQK +++R +  
Sbjct: 362 QSYYHAPFSKSGVLNQKYINDYARKLIEEYDVRTTGELVPAAALSGGNQQKAIIAREMDR 421

Query: 420 RPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRK 479
            P+ LI+ +PTRG+DVGA   I + +      G A+LV+S EL+E++  +DR+ ++   +
Sbjct: 422 DPELLIVSQPTRGLDVGAIEYIHKRLIEHRDKGKAVLVVSFELDEILNVSDRIAVIHAGE 481

Query: 480 QVAEIPLAELS 490
            V  +   E S
Sbjct: 482 IVGIVDPKETS 492



 Score =  109 bits (272), Expect = 3e-28
 Identities = 71/239 (29%), Positives = 127/239 (53%), Gaps = 16/239 (6%)

Query: 21  GVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAH 80
           G+ A+  +   +R GE++ + G +G G++ LI+A+TG+   ++GT+ ++G+ ++ +    
Sbjct: 272 GLDAVKGLSLDVRGGEVVGIAGIDGNGQTELIQAITGLRKVEKGTVTIKGKDVTNQRPRQ 331

Query: 81  AQQLGIGTVYQE---VNLLPNMSVADNL----FIGREPKRFGLLRRKEMEKRATELMASY 133
             ++GIG V ++     L+  MS+ADN+    +      + G+L +K +   A +L+  Y
Sbjct: 332 ITEVGIGHVPEDRHKYGLVLEMSLADNIALQSYYHAPFSKSGVLNQKYINDYARKLIEEY 391

Query: 134 GFSLDVRE-----PLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
               DVR      P    S   QQ   I R +D   ++LI+ +PT  LD   +E +   +
Sbjct: 392 ----DVRTTGELVPAAALSGGNQQKAIIAREMDRDPELLIVSQPTRGLDVGAIEYIHKRL 447

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247
            + RD+G +++ V+  LD++  VSDRI V+  G  VG  +  E  + EL  +M G  LD
Sbjct: 448 IEHRDKGKAVLVVSFELDEILNVSDRIAVIHAGEIVGIVDPKETSEKELGLLMAGYSLD 506


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: 644
Number of extensions: 37
Number of successful extensions: 7
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: 521
Length adjustment: 34
Effective length of query: 466
Effective length of database: 487
Effective search space:   226942
Effective search space used:   226942
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 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