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 GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha

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



>FitnessBrowser__WCS417:GFF3463
          Length = 502

 Score =  353 bits (907), Expect = e-102
 Identities = 201/473 (42%), Positives = 294/473 (62%), Gaps = 14/473 (2%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L+ E + K +PGV+AL +++  + RGEI ALLGENGAGKSTL+K L GV H D G I +
Sbjct: 4   LLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQILI 63

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGRE-PKRFGLLRRKEMEKRAT 127
           +GQA        A   GIG V+QE +L+P ++  +N+F+G E   RFGLLR++EM + + 
Sbjct: 64  DGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRKREMVEASE 123

Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187
            L    G ++D++  +   SVA QQ V I +A+ L A++L+LDEPTA+L   E ELLF++
Sbjct: 124 ALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELLFEI 183

Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL- 246
           MR+L+ +GV++IF++H L++++QV DRI+VLR+G  VG  +  +     LV+MM+GR L 
Sbjct: 184 MRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMMVGRRLA 243

Query: 247 ---DTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFD-LEVRPGEIVGLAGLLGSGRTET 302
                   +  G  LL  K +   +N        P +  ++  GEI+G AGL+GSGRTE 
Sbjct: 244 CSFPPKPTRERGPLLLEVKDIQLVRN-------GPHNRFQLHKGEILGFAGLVGSGRTEL 296

Query: 303 AEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIIL- 361
           A  + G  P+ S    ++G+   L  P QA   GIG  PE RK++G+I   S+RENI L 
Sbjct: 297 ALGMMGALPSVSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLN 356

Query: 362 ALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRP 421
            L   +     I +  +    E  ++QL I+ PS+E  +  LSGGNQQKV+++RW+    
Sbjct: 357 NLPKYQNASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHC 416

Query: 422 QFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVII 474
             L+ DEPTRGIDVGA A+I  L+ +L   G A+++ISSEL E++G  DRV +
Sbjct: 417 DVLVFDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAV 469



 Score = 84.7 bits (208), Expect = 7e-21
 Identities = 63/226 (27%), Positives = 109/226 (48%), Gaps = 9/226 (3%)

Query: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327
           K Y     +   +L+V  GEI  L G  G+G++   +++ G++  D G  LI G+ Q   
Sbjct: 12  KRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQILIDGQAQQFA 71

Query: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILA--LQAQRGWLRPISRKEQQEIAERF 385
           +   A   GIG   ++     +I   +  ENI L   L  + G LR   ++E  E +E  
Sbjct: 72  TYRDAIAAGIGIVFQEFS---LIPYLTAVENIFLGHELSNRFGLLR---KREMVEASEAL 125

Query: 386 IRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLI 445
            ++LG+ T   +  ++ LS   QQ V +++ L    + L+LDEPT  +       +  ++
Sbjct: 126 FKRLGV-TIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELLFEIM 184

Query: 446 ETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSV 491
             L   G+A++ IS  LEE+    DR+ ++RD   V    +A+  +
Sbjct: 185 RELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDI 230



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 58/221 (26%), Positives = 100/221 (45%), Gaps = 7/221 (3%)

Query: 30  FSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLGIGTV 89
           F L +GEI+   G  G+G++ L   + G   +    +WL G+ I+  + A A   GIG +
Sbjct: 275 FQLHKGEILGFAGLVGSGRTELALGMMGALPSVSKDVWLRGEKITLDDPAQALAHGIGLL 334

Query: 90  YQE---VNLLPNMSVADNLFIGREPK---RFGLLRRKEMEKRATELMASYGFSLDVREP- 142
            +      L+ + S+ +N+ +   PK     GL+ +         LM          E  
Sbjct: 335 PESRKSEGLITDFSIRENISLNNLPKYQNASGLIDKNRECASVEGLMKQLSIKAPSSESR 394

Query: 143 LNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSLIFVT 202
           +   S   QQ V I R I+    VL+ DEPT  +D      ++ LMR L ++G ++I ++
Sbjct: 395 VFNLSGGNQQKVVIARWINHHCDVLVFDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMIS 454

Query: 203 HFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243
             L ++  + DR+ V   G+ V   E   +   E+++   G
Sbjct: 455 SELPEIIGMCDRVAVFHKGAIVKLLEASAVNPQEVMRHATG 495


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: 575
Number of extensions: 25
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 500
Length of database: 502
Length adjustment: 34
Effective length of query: 466
Effective length of database: 468
Effective search space:   218088
Effective search space used:   218088
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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Candidates (tab-delimited)
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
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