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 GFF2162 PS417_11030 L-arabinose transporter ATP-binding protein

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



>FitnessBrowser__WCS417:GFF2162
          Length = 500

 Score =  345 bits (884), Expect = 3e-99
 Identities = 190/498 (38%), Positives = 303/498 (60%), Gaps = 23/498 (4%)

Query: 10  LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLE 69
           LR +G+ K FPGVKALD + FS   G++ AL+GENGAGKSTL+K L G Y  + GT+ + 
Sbjct: 6   LRFDGIGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNSGTLHIG 65

Query: 70  GQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATEL 129
            Q ++ K+ A +   G+  ++QE++L+P MSVA+NLF+G  P RFG++ R  + K+A   
Sbjct: 66  EQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLGHLPSRFGVVNRGLLRKQALAC 125

Query: 130 MASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMR 189
           +      +D  E L R S+  +Q+V I +A+   A V+  DEPT+SL  +E++ L  ++ 
Sbjct: 126 LKGLADEIDPAEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIA 185

Query: 190 QLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCE-LPQIELVKMMLGRELD- 247
           +LRD G  +++V+H +++V+++ + +TV ++G +V   E    L   +LV  M+GR++  
Sbjct: 186 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFEDMSALTHDQLVTCMVGRDIQD 245

Query: 248 --THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEV 305
              +  +  G   L    +         G   P    VR GEI+GL GL+G+GRTE   +
Sbjct: 246 IYDYRPREHGEVALKVDGLLG------PGLREPVSFNVRKGEILGLFGLVGAGRTELFRL 299

Query: 306 IFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA 365
           + G++ A +G   + G+P +L+SP  A   G+  CPEDRK +GII  +SV ENI ++ + 
Sbjct: 300 LSGLERASAGQLELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARG 359

Query: 366 QR---GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQ 422
                GWL  +    ++  A++ I  + ++TP+  Q I +LSGGNQQK +L RWL    +
Sbjct: 360 AHSTFGWL--LREGWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMK 417

Query: 423 FLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM------- 475
            L+LDEPTRGID+GA AEI ++I  L A G+A++V+SS+L E++G ADR++++       
Sbjct: 418 VLLLDEPTRGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRG 477

Query: 476 -RDRKQVAEIPLAELSVP 492
            + R+   E  L +L++P
Sbjct: 478 EQTREHATESNLLQLALP 495



 Score = 86.7 bits (213), Expect = 2e-21
 Identities = 72/253 (28%), Positives = 130/253 (51%), Gaps = 18/253 (7%)

Query: 5   QHQEI-LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADR 63
           +H E+ L+ +GL    PG++  + V F++R+GEI+ L G  GAG++ L + L+G+  A  
Sbjct: 253 EHGEVALKVDGL--LGPGLR--EPVSFNVRKGEILGLFGLVGAGRTELFRLLSGLERASA 308

Query: 64  GTIWLEGQAI---SPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKR--FGLLR 118
           G + L G+ +   SP++   A  L      ++  ++P  SVA+N+ I        FG L 
Sbjct: 309 GQLELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHSTFGWLL 368

Query: 119 RKEMEKRATELMASYGFSLDVREP-----LNRFSVAMQQIVAICRAIDLSAKVLILDEPT 173
           R+  EK   +   +   ++ V+ P     +   S   QQ   + R + +  KVL+LDEPT
Sbjct: 369 REGWEKGNADQQIN---AMKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMKVLLLDEPT 425

Query: 174 ASLDTQEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELP 233
             +D      ++ ++  L  +G+++I V+  L +V  ++DRI VL  G+  G +      
Sbjct: 426 RGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQTREHAT 485

Query: 234 QIELVKMMLGREL 246
           +  L+++ L R +
Sbjct: 486 ESNLLQLALPRSV 498


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: 613
Number of extensions: 28
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: 500
Length adjustment: 34
Effective length of query: 466
Effective length of database: 466
Effective search space:   217156
Effective search space used:   217156
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