GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Acidovorax sp. GW101-3H11

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate Ac3H11_444 Phosphoglucosamine mutase (EC 5.4.2.10)

Query= metacyc::MONOMER-13382
         (455 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_444
          Length = 444

 Score =  212 bits (540), Expect = 2e-59
 Identities = 147/439 (33%), Positives = 228/439 (51%), Gaps = 18/439 (4%)

Query: 5   FGTFGVRG-IANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALIS 63
           FGT G+RG +    ITP+F +++  A G +L R+  ++P V++G+DTR+SG ML+ AL S
Sbjct: 6   FGTDGIRGTVGQPPITPDFVLRLAHAVGRVL-RQTEERPTVLIGKDTRISGYMLESALES 64

Query: 64  GLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123
           G  S G DV+ +G  PTP V + T+   A  G VI+ASHNP   NGIK     G  L   
Sbjct: 65  GFNSAGVDVVLLGPLPTPGVAYLTRAQRASLGVVISASHNPYPDNGIKFFSAQGTKLSDA 124

Query: 124 REAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPFVVVDTS 182
            E  VEE   +     A    +G+ RR +D    YIE  KS    +   K    +VVD +
Sbjct: 125 WELAVEEALAQSPV-WADSASLGKARRLDDAAGRYIEFCKSTFPQDLTLKGLK-IVVDAA 182

Query: 183 NGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVAQ 242
           +GA     P +  ELG +V+++   PDG     N E    +    +  V+A  AD+G+A 
Sbjct: 183 HGAAYQVAPKVFHELGAEVLSIGCAPDGL--NINHEVGATHPDALVRAVRANRADYGIAL 240

Query: 243 DGDADRAVFIDENGRFIQGDKTFALVA-DAVLKEKGGGLLVTTVATSNLLDDIAKKHGAK 301
           DGDADR   +D  GR   GD+   L+A D + +++    +V T+ T+  ++   +  G K
Sbjct: 241 DGDADRLQVVDATGRLYNGDELLYLMASDRMGRDEHVPGVVGTLMTNMAVEVALQSRGVK 300

Query: 302 VMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKFS 361
            +R KVGD  V   L  +   +GGE +G ++  +     DG ++  +V++   +SG+  +
Sbjct: 301 FVRAKVGDRYVLEELARHRWLLGGEGSGHLLALDRHTTGDGLVSALQVLQACVRSGQTLA 360

Query: 362 ELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGA-KIIFEDGWVLVRA 420
           +L+ E+  Y Q+     +   +    N++           DTT    + +   G VL+RA
Sbjct: 361 QLLAEVTLYPQVLLNVRLAPGQDWKSNRL---------LADTTQAVERDLGASGRVLIRA 411

Query: 421 SGTEPIIRIFSEAKSKEKA 439
           SGTEP++R+  EA+  E A
Sbjct: 412 SGTEPLLRVMVEARDAEMA 430


Lambda     K      H
   0.317    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: 445
Number of extensions: 23
Number of successful extensions: 5
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: 455
Length of database: 444
Length adjustment: 33
Effective length of query: 422
Effective length of database: 411
Effective search space:   173442
Effective search space used:   173442
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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:

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