Alignments for a candidate for ytfR in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Pseudomonas simiae WCS417

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

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



>FitnessBrowser__WCS417:GFF2332
          Length = 517

 Score =  365 bits (937), Expect = e-105
 Identities = 193/488 (39%), Positives = 301/488 (61%), Gaps = 4/488 (0%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L    +SK FPGV AL +V   +R G ++AL+GENGAGKSTL+K + G+Y  D G I L
Sbjct: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREP-KRFGLLRRKEMEKRAT 127
            G+ I  +    AQ+ GI  ++QE+NL+P+MS+A+N++IGRE      ++  +EM +   
Sbjct: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142

Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187
           EL+A    +LD  E +   S+A +Q+V I +A+   + +LI+DEPT+++  +EV  LF +
Sbjct: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202

Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247
           +  L+ +G  ++++TH +++V+ ++D + V R+G ++G +    +    L+ MM+GREL 
Sbjct: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262

Query: 248 THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307
              L     T + D  +   ++    G       ++  GEI+G+AGL+GSGRT  AE IF
Sbjct: 263 Q--LFPLRETPIGDL-LLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319

Query: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR 367
           GI P+ SG   + GK   +  PH A   G     EDRK  G+    SV EN+ +A+    
Sbjct: 320 GITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379

Query: 368 GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILD 427
                I +K  + + E   ++L ++TPS EQ I+ LSGGNQQK LL+RWL+T P+ LILD
Sbjct: 380 TGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILD 439

Query: 428 EPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLA 487
           EPTRGIDVGA AEI RLI  L ++G+A+++ISSEL E++G +DRV++M + + +  +  +
Sbjct: 440 EPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRS 499

Query: 488 ELSVPAIM 495
           E +   +M
Sbjct: 500 EATQEKVM 507



 Score = 78.2 bits (191), Expect = 7e-19
 Identities = 52/223 (23%), Positives = 110/223 (49%), Gaps = 6/223 (2%)

Query: 27  NVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLGI 86
           +V F L  GEI+ + G  G+G++ + + + G+  +  G I L+G+A+   +   A + G 
Sbjct: 290 DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGF 349

Query: 87  GTVYQE---VNLLPNMSVADNLFIGREPKRFG--LLRRKEMEKRATELMASYGFSL-DVR 140
             + ++     L P +SV +N+ +   P   G   +++K +     ++          + 
Sbjct: 350 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLE 409

Query: 141 EPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSLIF 200
           + ++  S   QQ   + R +  + ++LILDEPT  +D      ++ L+  L   G+++I 
Sbjct: 410 QCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIM 469

Query: 201 VTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243
           ++  L +V  +SDR+ V+  G  +G  +  E  Q +++++  G
Sbjct: 470 ISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512


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: 561
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: 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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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