GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araVsh in Bradyrhizobium sp. BTAi1

Align ABC transporter related (characterized, see rationale)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>NCBI__GCF_000015165.1:WP_012042345.1
          Length = 516

 Score =  499 bits (1285), Expect = e-146
 Identities = 259/494 (52%), Positives = 346/494 (70%), Gaps = 2/494 (0%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           +LE++ ++K +  +KAL+DV   L  GE+HALLGENGAGKSTL+KV+TG  ++D G +  
Sbjct: 14  LLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDAGTVRL 73

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            G+     +  DA +AGI+TVYQEVNL+PNL+VAQNL+LG +P R G++   +M   A A
Sbjct: 74  AGDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRFGVVRQAEMRRRAHA 133

Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
           +L  + LDIDV APL+ YS+AVQ + AIAR V +SA+VL+LDEPTASLD  EV++LF ++
Sbjct: 134 LLLDYGLDIDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTASLDRHEVEILFRVM 193

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243
            +L A G+ IVF++HFLDQVY+I DR+TVLRNG+ IG     +LP+  LI  MLGR L E
Sbjct: 194 RKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRDITDLPRLDLIRMMLGRELAE 253

Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303
              ++   +    R   V +S +    +G +   +L + +G+ VGLAGLLGSGR+E    
Sbjct: 254 TTHERAASQPDTAR--EVCVSFKGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETARL 311

Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQA 363
           VFG +  DSG   +AG+ + L+ P DA   G   CPE+RK +GI+  L++RENI+LALQA
Sbjct: 312 VFGAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLALQA 371

Query: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423
           R G  R LS   Q EIA  +I  L I  PD ++PI  LSGGNQQK +LARWLA  P LLV
Sbjct: 372 RRGLHRPLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQQKALLARWLATSPKLLV 431

Query: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELS 483
           LDEPTRGID+GAHAEI++L+R LC++G++LLV SSELDE+V +SN+VVVLRDR  V EL 
Sbjct: 432 LDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTYSNRVVVLRDRAHVEELK 491

Query: 484 GAELTSQHVMQAIA 497
           G  +    ++ AIA
Sbjct: 492 GDAVEVSSILAAIA 505


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: 640
Number of extensions: 23
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 499
Length of database: 516
Length adjustment: 34
Effective length of query: 465
Effective length of database: 482
Effective search space:   224130
Effective search space used:   224130
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 Apr 09 2024. 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:

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:

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:

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:

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