GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Sinorhizobium meliloti 1021

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate SMc00637 SMc00637 phosphoglucosamine mutase

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



>FitnessBrowser__Smeli:SMc00637
          Length = 450

 Score =  219 bits (557), Expect = 2e-61
 Identities = 147/453 (32%), Positives = 237/453 (52%), Gaps = 30/453 (6%)

Query: 3   KLFGTFGVRGIANE-KITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEAL 61
           + FGT G+RG +N   +TP+ AM++G+A GT+  R G  +  VV+G+DTR+SG ML+ A+
Sbjct: 4   RYFGTDGIRGQSNIFPMTPDLAMRVGIAVGTIF-RNGAHRHRVVIGKDTRLSGYMLENAM 62

Query: 62  ISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
           ++G  + G DV  +G  PTP V   T+   AD G +I+ASHN    NGIKL  P+G  L 
Sbjct: 63  VAGFTAAGLDVFLLGPIPTPGVAMLTRSLRADIGVMISASHNAFRDNGIKLFGPDGYKLS 122

Query: 122 KEREAIVEELFFKE-DFDRAKWYEIGEVRRED-IIKPYIEAIKSKVDVEAIKKRKPFVVV 179
            + E  +E+L  ++     AK  +IG  +R D  I  YIE  K  +  +   K    + +
Sbjct: 123 DDIEQKIEDLLEQDMSGQLAKPEDIGRAKRVDGDIYRYIEQAKRTLPRDVTLKGLR-IAI 181

Query: 180 DTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFG 239
           D +NGA     P  L ELG +V+T+  +P+G     N E    +     + V  + AD G
Sbjct: 182 DCANGAAYKVAPSALWELGAEVVTIGTEPNGV--NINLECGSTHPAALQKKVHEVRADIG 239

Query: 240 VAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKE---KGGGLLVTTVATSNL-LDDIA 295
           +A DGDADR + +DE G  I GD+  A++AD+   +   KGGG+  T +  SNL L+   
Sbjct: 240 IALDGDADRVLIVDEEGAVIDGDQLMAVIADSWAADGMLKGGGIAATVM--SNLGLERYL 297

Query: 296 KKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAK 355
           +    K+ RTKVGD  V   + ++   +GGE++G ++  +     DG +   +++ +  +
Sbjct: 298 QARRLKLHRTKVGDRYVVEQMRQDGLNVGGEQSGHIVLSDFGTTGDGLVAALQILAVVKR 357

Query: 356 SGKKFSELIDELPKYYQIKTKRHVEGDR----HAIVNKVAEMARERGYTVDTTDGAKIIF 411
            GK  SE+        Q+     V   +     A+   +AE   +             + 
Sbjct: 358 QGKTVSEICRRFEPVPQVLKNVRVSAGKPLEDAAVQQAIAEAEAQ-------------LA 404

Query: 412 EDGWVLVRASGTEPIIRIFSEAKSKEKAQEYLN 444
           ++G +L+R SGTEP+IR+ +E   + + +  ++
Sbjct: 405 KNGRLLIRPSGTEPLIRVMAEGDDRGQVERIVD 437


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: 546
Number of extensions: 27
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: 455
Length of database: 450
Length adjustment: 33
Effective length of query: 422
Effective length of database: 417
Effective search space:   175974
Effective search space used:   175974
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