Alignments for a candidate for araVsh in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Sinorhizobium meliloti 1021

Align ABC transporter related (characterized, see rationale)
to candidate SM_b21588 SM_b21588 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__Smeli:SM_b21588
          Length = 505

 Score =  503 bits (1296), Expect = e-147
 Identities = 265/494 (53%), Positives = 343/494 (69%), Gaps = 4/494 (0%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           IL   +I K +PG KAL+ V   L  GEVHALLGENGAGKSTL+K +TGA  +D G +L 
Sbjct: 8   ILSATRIEKGFPGTKALDRVDFHLRRGEVHALLGENGAGKSTLIKCLTGAYRRDGGSMLL 67

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            G         DAQ+ GI TVYQEVNL+PNLTVA+NLFLG +PRR G++  + M   AR 
Sbjct: 68  DGAEADPRDTFDAQRLGIGTVYQEVNLLPNLTVAENLFLGRQPRRFGMVDTRTMNRKARE 127

Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
           +L +++LDIDV+  L+ YS+A+QQ++AIAR V +S KVL+LDEPTASLDA EV++LF I+
Sbjct: 128 LLAEYELDIDVTRDLASYSVAIQQVVAIARAVDLSGKVLILDEPTASLDAHEVEMLFRIV 187

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243
            +LK +G+ I+FITHFL+QVY ISDRITVLRNGQ +G    A+L + +LI  M+GR L  
Sbjct: 188 RRLKERGLGIIFITHFLEQVYAISDRITVLRNGQLVGTRNAADLDRRELIAMMIGRELAT 247

Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303
           ++        +   A        +   +G I   +L V  G+ VG+AGLLGSGR+E    
Sbjct: 248 EI----HSAHSDAVAGEPRYRFRNFGRRGKIDPFDLDVRAGEVVGMAGLLGSGRTETAEI 303

Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQA 363
           +FG    DSG+  + G+ ++LS P  AI      CPEDRK  GI+G LS+RENI+LALQA
Sbjct: 304 LFGAHRADSGTAEIDGRSVDLSSPRAAIRQKFGFCPEDRKTAGIVGDLSVRENIVLALQA 363

Query: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423
           R GW R +    Q  +A  +I  L I T D +KPI  LSGGNQQK ILARWLA EP LL+
Sbjct: 364 RRGWTRPIPRAEQNRLADHYIRALDIRTADREKPIRLLSGGNQQKAILARWLATEPELLI 423

Query: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELS 483
           LDEPTRGID+GAHAEI++LI +L ++GMSL+V SSE++ELVA+S +VVVLRD   V EL 
Sbjct: 424 LDEPTRGIDVGAHAEIIRLIESLREKGMSLIVISSEIEELVAYSTRVVVLRDHAHVAELD 483

Query: 484 GAELTSQHVMQAIA 497
           GA+LT+  +++AIA
Sbjct: 484 GAQLTAHRIVEAIA 497



 Score = 74.7 bits (182), Expect = 7e-18
 Identities = 59/230 (25%), Positives = 111/230 (48%), Gaps = 6/230 (2%)

Query: 20  LEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMDA--Q 77
           ++   L + AGEV  + G  G+G++   +++ GA   D G     G     ++P  A  Q
Sbjct: 274 IDPFDLDVRAGEVVGMAGLLGSGRTETAEILFGAHRADSGTAEIDGRSVDLSSPRAAIRQ 333

Query: 78  KAGISTVYQEV-NLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAVLTQFKLDI---D 133
           K G     ++   +V +L+V +N+ L  + RR       +   +  A      LDI   D
Sbjct: 334 KFGFCPEDRKTAGIVGDLSVRENIVLALQARRGWTRPIPRAEQNRLADHYIRALDIRTAD 393

Query: 134 VSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAKGVAI 193
              P+   S   QQ   +AR +A   ++L+LDEPT  +D      +  ++  L+ KG+++
Sbjct: 394 REKPIRLLSGGNQQKAILARWLATEPELLILDEPTRGIDVGAHAEIIRLIESLREKGMSL 453

Query: 194 VFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243
           + I+  ++++   S R+ VLR+   + E   A+L   +++EA+   + +E
Sbjct: 454 IVISSEIEELVAYSTRVVVLRDHAHVAELDGAQLTAHRIVEAIAATNGRE 503


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: 668
Number of extensions: 28
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: 505
Length adjustment: 34
Effective length of query: 465
Effective length of database: 471
Effective search space:   219015
Effective search space used:   219015
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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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