GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Pantoea rwandensis LMG 26275

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_084932744.1 HA51_RS05190 ribose ABC transporter ATP-binding protein RbsA

Query= uniprot:A0A165ZSX8
         (514 letters)



>NCBI__GCF_002095475.1:WP_084932744.1
          Length = 502

 Score =  403 bits (1036), Expect = e-117
 Identities = 220/493 (44%), Positives = 328/493 (66%), Gaps = 3/493 (0%)

Query: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75
           L+  GI KSFPGV+AL   S   +PG+V AL+GENGAGKST++K+L G Y   +G LQ  
Sbjct: 5   LQLKGIEKSFPGVKALNGASLAVYPGRVMALVGENGAGKSTMMKVLTGIYSMDAGSLQWL 64

Query: 76  EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGH-LPARFGLVNRGVLRQQALT 134
            + +AF G   S  +G+ +IHQEL+L+P++TVAEN+FLG     RFG +    +  +A  
Sbjct: 65  GKDVAFSGPKASQEAGIGIIHQELNLIPQLTVAENIFLGREFVNRFGRIEWNRMYAEADA 124

Query: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194
           LL  L    +  + VG LS+G +Q+VEIAK LS  + VI  DEPT +L+  E   L  +I
Sbjct: 125 LLHRLNLRFNSHKLVGDLSIGDQQMVEIAKVLSFESQVIIMDEPTDALTDTETLSLFRVI 184

Query: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254
             L+ +G  ++Y+SHRM+E+F IC+ VTVF+DG+++     +S+L+ + L+  MVGR ++
Sbjct: 185 NELKAQGCGIVYISHRMKEIFEICDDVTVFRDGQFIAE-RAVSDLSEESLIEMMVGRKLE 243

Query: 255 DIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLE 314
           D Y +  +  GD+ L V+ L GPG+ + VSF + KGEILG+ GL+GAGRTEL+++L G  
Sbjct: 244 DQYPHIDQAPGDIRLTVEHLSGPGV-DNVSFNLRKGEILGISGLMGAGRTELMKVLYGAL 302

Query: 315 RQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTL 374
            + +G++ L+ +E+  RSP+D +A G++   EDRK++G++   SV EN++++A    S  
Sbjct: 303 PRSKGTVTLNGREIMTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSHA 362

Query: 375 GCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434
              L+   E+      I+   VKTP+  Q I  LSGGNQQK  + R L     VL+LDEP
Sbjct: 363 TGNLKHSEEQLAVGDFIRLFNVKTPSMEQPIGLLSGGNQQKVAIARGLMTRPNVLILDEP 422

Query: 435 TRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQA 494
           TRG+D+GAK EIYQ+I+   A+G+++I+VSS++ EV+G+SDRILV+ EG + GE SR+QA
Sbjct: 423 TRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRILVMHEGHLSGEFSREQA 482

Query: 495 NESNLLQLALPRQ 507
            + +L+  A+ +Q
Sbjct: 483 TQESLMAAAVGKQ 495


Lambda     K      H
   0.320    0.138    0.391 

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: 693
Number of extensions: 34
Number of successful extensions: 9
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: 514
Length of database: 502
Length adjustment: 34
Effective length of query: 480
Effective length of database: 468
Effective search space:   224640
Effective search space used:   224640
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:

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