Alignments for a candidate for araVsh in Ochrobactrum thiophenivorans DSM 7216

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Ochrobactrum thiophenivorans DSM 7216

Align ABC transporter related (characterized, see rationale)
to candidate WP_169717299.1 CEV31_RS02620 sugar ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>NCBI__GCF_002252445.1:WP_169717299.1
          Length = 517

 Score =  493 bits (1270), Expect = e-144
 Identities = 263/495 (53%), Positives = 346/495 (69%), Gaps = 2/495 (0%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           +LE + I+K + GV AL+ V   L  GE+HALLGENGAGKSTL+K++TGA     G +L 
Sbjct: 16  LLEARSITKSFLGVTALDRVDFVLNRGEIHALLGENGAGKSTLIKILTGAYHGFDGSVLL 75

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            G      +  +AQ  GI TVYQEVNL+ NLTVA+NLFLG +PRR G I  ++M   A  
Sbjct: 76  DGHAIAPASVAEAQTLGIGTVYQEVNLLENLTVAENLFLGRQPRRFGFIDRRRMEKHATT 135

Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
           +L ++ L IDV APLS YS+A++Q+IAIAR V +S KVLVLDEPTASLDA EV++LFG+L
Sbjct: 136 LLARYGLTIDVGAPLSAYSVAIRQIIAIARAVDVSGKVLVLDEPTASLDAHEVEMLFGVL 195

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243
            QL+A+G+ I+ ITHFLDQVY I+D  TVLRNG+ +G    +ELP+  LI  MLG  LQE
Sbjct: 196 RQLQAEGLGIIIITHFLDQVYAIADSATVLRNGRLVGSRDLSELPRTDLISMMLGHQLQE 255

Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303
            +  ++     V+      +       KGS+   +L +  G+AVG+AGLLGSGR+E    
Sbjct: 256 TV--RRHLTEDVSDNTTAPIRFSGFGKKGSVAPFDLAIKPGEAVGIAGLLGSGRTETALL 313

Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQA 363
           +FG+D  DSG++ + G+   L  PV AI+   A CPE+RK DGIIG  S+ ENI LA+QA
Sbjct: 314 MFGVDQSDSGTLTIDGKDTKLPSPVAAIAERFAFCPEERKSDGIIGDFSVAENIALAVQA 373

Query: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423
           + GW + +S+  +  +A+ +I  L I  PD +KPI+ LSGGNQQK ILARWLA +P LL+
Sbjct: 374 KRGWSKPISSREKNALAERYIKALDIRPPDPNKPIKLLSGGNQQKAILARWLATDPRLLI 433

Query: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELS 483
           LDEPTRGIDIGAHAEI+KLI  LC EGMSL++ SSE +EL A +N+VVVL DR  V EL 
Sbjct: 434 LDEPTRGIDIGAHAEILKLIGELCTEGMSLVIISSEFEELAAVANRVVVLSDRRHVAELK 493

Query: 484 GAELTSQHVMQAIAE 498
           G E+T+ ++++AIA+
Sbjct: 494 GEEITADNIVRAIAD 508



 Score = 65.9 bits (159), Expect = 3e-15
 Identities = 50/228 (21%), Positives = 105/228 (46%), Gaps = 6/228 (2%)

Query: 25  LRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMDAQKAGISTV 84
           L +  GE   + G  G+G++    +M G    D G +   G+     +P+ A     +  
Sbjct: 289 LAIKPGEAVGIAGLLGSGRTETALLMFGVDQSDSGTLTIDGKDTKLPSPVAAIAERFAFC 348

Query: 85  YQEVN---LVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAVLTQFKLDI---DVSAPL 138
            +E     ++ + +VA+N+ L  + +R           +A A      LDI   D + P+
Sbjct: 349 PEERKSDGIIGDFSVAENIALAVQAKRGWSKPISSREKNALAERYIKALDIRPPDPNKPI 408

Query: 139 SDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAKGVAIVFITH 198
              S   QQ   +AR +A   ++L+LDEPT  +D      +  ++ +L  +G+++V I+ 
Sbjct: 409 KLLSGGNQQKAILARWLATDPRLLILDEPTRGIDIGAHAEILKLIGELCTEGMSLVIISS 468

Query: 199 FLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQEQLV 246
             +++  +++R+ VL + + + E    E+    ++ A+     +++ V
Sbjct: 469 EFEELAAVANRVVVLSDRRHVAELKGEEITADNIVRAIADTGSEKEAV 516


Lambda     K      H
   0.319    0.136    0.377 

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: 622
Number of extensions: 23
Number of successful extensions: 6
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: 499
Length of database: 517
Length adjustment: 34
Effective length of query: 465
Effective length of database: 483
Effective search space:   224595
Effective search space used:   224595
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 24 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 2024 update 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