Alignments for a candidate for ytfR in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Phaeobacter inhibens BS107

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

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



>FitnessBrowser__Phaeo:GFF2274
          Length = 503

 Score =  336 bits (861), Expect = 1e-96
 Identities = 185/499 (37%), Positives = 296/499 (59%), Gaps = 10/499 (2%)

Query: 5   QHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRG 64
           +   +LR EG+ K FPGV+ALD V  ++  GE+ AL+GENGAGKSTL+K L G++  D G
Sbjct: 3   EQSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEG 62

Query: 65  TIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREP-KRFGLLRRKEME 123
            I +  Q +       A+  GI  ++QE++L   +SVA+N+++G  P KRFGL+   E+E
Sbjct: 63  QIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELE 122

Query: 124 KRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVEL 183
            +   ++       + +  +   S+A QQ+V I RA+ + AK +I DEPTASL   E  +
Sbjct: 123 AKTNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVV 182

Query: 184 LFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243
           LF+++  L+++GV + +++H ++++++++DRI+VLR+G + G   T E  +  + +MM+G
Sbjct: 183 LFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIG 242

Query: 244 RELD---THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRT 300
           R+LD     A    G   L  + ++              + EVR GE+VG  GL+G+GRT
Sbjct: 243 RKLDLSRNEAHHELGEVALEVRGLSC------GSLFEDVNFEVRRGEVVGFYGLVGAGRT 296

Query: 301 ETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENII 360
           E AE +FG++   SG+  + G    + SPH A   GI   PEDRK  G++   + R+N+ 
Sbjct: 297 EIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMT 356

Query: 361 LALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTR 420
           L           ++   +  I +++  +L IRTP  +Q +  LSGGNQQK+++ +WL  R
Sbjct: 357 LPQVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMR 416

Query: 421 PQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQ 480
           P  LI+DEPTRGIDVG+ AEI  L+  L A G A++VISSE+ E++  ADR++ M   + 
Sbjct: 417 PNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRI 476

Query: 481 VAEIPLAELSVPAIMNAIA 499
           +      E++   ++ AI+
Sbjct: 477 MRTFTSEEVTEENLIAAIS 495



 Score = 79.0 bits (193), Expect = 4e-19
 Identities = 60/232 (25%), Positives = 116/232 (50%), Gaps = 14/232 (6%)

Query: 26  DNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLG 85
           ++V+F +RRGE++   G  GAG++ + + L G+ +   G+I+L+G  ++  +   A + G
Sbjct: 273 EDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERG 332

Query: 86  IGTVYQE---VNLLPNMSVADNLFIGR-EPKRFGLLRRKEMEKRATELMASYGFSLDVRE 141
           I  V ++     L+  M+  DN+ + + +  + G       E     +   Y   LD+R 
Sbjct: 333 ISLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAE---IAIFDQYRDKLDIRT 389

Query: 142 P-----LNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGV 196
           P     +   S   QQ + I + + +   VLI+DEPT  +D      + +L+R L  +G 
Sbjct: 390 PGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGY 449

Query: 197 SLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248
           ++I ++  + +V  V+DRI  + +G  +    + E+ +  L+  + G  LDT
Sbjct: 450 AVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISG--LDT 499


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: 622
Number of extensions: 47
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: 503
Length adjustment: 34
Effective length of query: 466
Effective length of database: 469
Effective search space:   218554
Effective search space used:   218554
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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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 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