GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Pontibacter ramchanderi LP43

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_101446908.1 BD749_RS17540 gliding motility-associated ABC transporter ATP-binding subunit GldA

Query= uniprot:B2SYR5
         (512 letters)



>NCBI__GCF_002846395.1:WP_101446908.1
          Length = 303

 Score =  107 bits (267), Expect = 6e-28
 Identities = 71/212 (33%), Positives = 110/212 (51%), Gaps = 6/212 (2%)

Query: 9   NIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEV 68
           N+ K+F   RA+D +SF V+ GQ+ G +G NGAGKST +KI      P +G V++ G +V
Sbjct: 7   NLTKLFGSQRAVDDISFSVSQGQILGFLGPNGAGKSTTMKIATCYLPPSAGTVLVAGYDV 66

Query: 69  RFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRERLEAM 128
                A     G    H  L    D+ V E L   Q   S+  +  R AK  V E +E  
Sbjct: 67  LQDPIAVRRNVGYLPEHNPLYL--DMYVHEYL---QFVASVYGLKGRLAKERVHEMVELC 121

Query: 129 GVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVRDLRA 188
           G+ L+   K+  LS   RQ V + +AL+ + +V+ LDEPT+ L   +   +  L++ +  
Sbjct: 122 GLTLEQGKKIGALSKGYRQRVGLAQALVHDPQVLILDEPTTGLDPNQIVEIRSLIKRIGQ 181

Query: 189 DNRAMIYISHRMDEIYELCDACTIFRDGRKIA 220
           D + +I+ +H M E+  +CD   I   G+ +A
Sbjct: 182 D-KTVIFSTHIMQEVTAICDRVVIINRGKLVA 212



 Score = 58.5 bits (140), Expect = 3e-13
 Identities = 58/221 (26%), Positives = 102/221 (46%), Gaps = 14/221 (6%)

Query: 255 EVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDG 314
           EV+   K           SF V +G+I+GF G  GAG+S  M +         G +L+ G
Sbjct: 4   EVKNLTKLFGSQRAVDDISFSVSQGQILGFLGPNGAGKSTTMKIATCYLPPSAGTVLVAG 63

Query: 315 KPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAE 374
               V     A+R  +   PE      +     V E +      + L+  +  +R  E  
Sbjct: 64  --YDVLQDPIAVRRNVGYLPE---HNPLYLDMYVHEYLQFVASVYGLKGRLAKERVHE-- 116

Query: 375 TADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKH 434
                ++L  + T  + +KI  LS G +Q+  L++ L   D +V+ILDEPT G+D     
Sbjct: 117 ----MVELCGL-TLEQGKKIGALSKGYRQRVGLAQALVH-DPQVLILDEPTTGLDPNQIV 170

Query: 435 EIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRI 475
           EI ++I ++ +    ++  +  + EV  + DR+V++ +G++
Sbjct: 171 EIRSLIKRIGQ-DKTVIFSTHIMQEVTAICDRVVIINRGKL 210


Lambda     K      H
   0.320    0.136    0.385 

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: 289
Number of extensions: 17
Number of successful extensions: 4
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: 512
Length of database: 303
Length adjustment: 31
Effective length of query: 481
Effective length of database: 272
Effective search space:   130832
Effective search space used:   130832
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: 50 (23.9 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:

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