Alignments for a candidate for xylK_Tm in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Desulfovibrio vulgaris Hildenborough

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  272 bits (695), Expect = 3e-77
 Identities = 172/496 (34%), Positives = 269/496 (54%), Gaps = 19/496 (3%)

Query: 6   AFRGDRMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLK 65
           A R D   +++ +GI K F  V A  ++  ++    I +L+GENGAGKSTL+ IL+G L 
Sbjct: 26  ALRHDVTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLA 85

Query: 66  PDAGEILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLS 125
            D G I V+GE V F SP DA K GI +++Q   L D+MTVAEN+ L      GQ     
Sbjct: 86  QDTGIIHVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLL------GQSGAWL 139

Query: 126 SRVDENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTS 185
           S V   +M     EL    G    P A V +L+  +RQ VEI K L ++ R++ +DEPT+
Sbjct: 140 SPV---HMSRVVAELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTA 196

Query: 186 SLTVEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDV 245
            LT  ETE+LFE +  +   G ++VF+SH++ EV+ ++D I ++R G+ + E  + E   
Sbjct: 197 VLTPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPG 256

Query: 246 DT-IIKMMVGREVEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVG 304
           +  +   MVGREV          PG+  L V  L   D +K +SFEVRKGEV   AG+ G
Sbjct: 257 EAELANRMVGREVILEVAAEPLEPGDRVLHVDGLA-GDGLKGLSFEVRKGEVFAIAGVAG 315

Query: 305 AGRTETMLLVFGVNQKESGDIYVNG---RKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRM 361
            G+ E +  V G+ +   G++ + G   R+   K P      G+  IPEDR+     L +
Sbjct: 316 NGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG---GLAYIPEDRQGLATCLSL 372

Query: 362 TVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVV 421
            + DN +L +    +R G  LD +  +  + D +   +++         +LSGGN QK+V
Sbjct: 373 DLVDNFLLTARGCFTR-GPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLV 431

Query: 422 LAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRI 481
           + +       +++ + PT+G+D+ A  E+   + E+ +    V+++S +L E+L L+DR+
Sbjct: 432 VGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA-GVLLVSGDLNEVLALADRV 490

Query: 482 VVMWEGEITAVLDNRE 497
            VM+ G    +LD  +
Sbjct: 491 AVMYRGCFIGLLDRSD 506



 Score = 64.3 bits (155), Expect = 1e-14
 Identities = 57/231 (24%), Positives = 108/231 (46%), Gaps = 10/231 (4%)

Query: 33  VDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGIS 92
           + FEV + E+ ++ G  G G+  L++ +TG+ +P  GE+ + G            + G++
Sbjct: 298 LSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLA 357

Query: 93  VI---HQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKFS 149
            I    Q L  C ++ + +N  L          T    +D       ++++L     +  
Sbjct: 358 YIPEDRQGLATCLSLDLVDNFLLTARGCF----TRGPFLDRKSADAAARDILAEYNVQPG 413

Query: 150 -PDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGIS 208
             +A  R+L+    Q + + +   ++P +I  + PT  L +  TE ++  +  ++S    
Sbjct: 414 RAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA-G 472

Query: 209 VVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFD-VDTIIKMMVGREVE 258
           V+ VS  L+EV+ ++DR+ VM  G  IG L + + + VD I  MM G   E
Sbjct: 473 VLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMMAGVSCE 523


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: 653
Number of extensions: 45
Number of successful extensions: 10
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: 524
Length adjustment: 35
Effective length of query: 485
Effective length of database: 489
Effective search space:   237165
Effective search space used:   237165
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