Alignments for a candidate for xylK_Tm in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Phaeobacter inhibens BS107

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Phaeo:GFF2274
          Length = 503

 Score =  422 bits (1084), Expect = e-122
 Identities = 225/502 (44%), Positives = 329/502 (65%), Gaps = 8/502 (1%)

Query: 10  DRMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAG 69
           ++  +L+ +GIVK FPGV A+D V   +   E+ +L+GENGAGKSTL+K+L G+ +PD G
Sbjct: 3   EQSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEG 62

Query: 70  EILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVD 129
           +I+V  + V    P+DA  KGI  IHQEL+L D ++VAENI+L         R     VD
Sbjct: 63  QIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGE-----LPRKRFGLVD 117

Query: 130 ENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTV 189
              +  ++  +L+ +   F+    V +L+ A +QMVEI +AL  + + +  DEPT+SLT 
Sbjct: 118 WAELEAKTNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTD 177

Query: 190 EETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTII 249
            E   LFE+I  L+ +G+ + ++SHR++E+ +I+DRI V+RDG+  G +   E + + + 
Sbjct: 178 AEKVVLFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVT 237

Query: 250 KMMVGREVEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTE 309
           +MM+GR+++   +      GE+ALEVR L      ++V+FEVR+GEV+GF GLVGAGRTE
Sbjct: 238 QMMIGRKLDLSRNEAHHELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTE 297

Query: 310 TMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVL 369
               +FG+    SG I+++G +V I +P DAI+ GI L+PEDRK QGLVL M  +DN+ L
Sbjct: 298 IAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTL 357

Query: 370 PSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATN 429
           P +  +     V D   E  I + Y  +L I+TP   Q+  NLSGGNQQK+V+ KWL+  
Sbjct: 358 PQVDDLKAGPFVAD-GAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMR 416

Query: 430 ADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEI 489
            ++LI DEPTRGIDVG+KAEIH ++R+LAAQG AVI+ISSE+PE+L+++DRIV M+ G I
Sbjct: 417 PNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRI 476

Query: 490 TAVLDNREKRVTQEEIMYYASG 511
                + E  VT+E ++   SG
Sbjct: 477 MRTFTSEE--VTEENLIAAISG 496



 Score = 94.7 bits (234), Expect = 7e-24
 Identities = 62/237 (26%), Positives = 117/237 (49%), Gaps = 18/237 (7%)

Query: 31  DNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKG 90
           ++V+FEV   E+V   G  GAG++ + + L G+  P +G I ++G  V   SP DA ++G
Sbjct: 273 EDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERG 332

Query: 91  ISVIHQE---------LNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELL 141
           IS++ ++         +N  DNMT+ +   L           ++       ++ + ++ L
Sbjct: 333 ISLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIA-------IFDQYRDKL 385

Query: 142 DLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEM 201
           D+    +    LV NL+   +Q + I K L   P ++ +DEPT  + V     +  ++  
Sbjct: 386 DIRTPGWKQ--LVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRD 443

Query: 202 LKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREVE 258
           L ++G +V+ +S  + EV+ ++DRIV M  G+ +      E   + +I  + G + E
Sbjct: 444 LAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLDTE 500


Lambda     K      H
   0.319    0.138    0.381 

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: 697
Number of extensions: 38
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: 520
Length of database: 503
Length adjustment: 35
Effective length of query: 485
Effective length of database: 468
Effective search space:   226980
Effective search space used:   226980
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 (21.7 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