GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Collinsella tanakaei YIT 12063

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_009140673.1 HMPREF9452_RS03215 phosphoglucosamine mutase

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



>NCBI__GCF_000225705.1:WP_009140673.1
          Length = 447

 Score =  177 bits (450), Expect = 5e-49
 Identities = 138/458 (30%), Positives = 213/458 (46%), Gaps = 25/458 (5%)

Query: 3   KLFGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALI 62
           K FGT G RG ANE +  + A KIG   G        KK  V++G+DTR+S  M + AL+
Sbjct: 2   KYFGTDGFRGRANEGLNVDHAFKIGRFVGWYYGARRGKKARVIIGKDTRLSSYMFESALV 61

Query: 63  SGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKK 122
           SGL++ G D   + + PTP V +       D G +ITASHNP   NGIKL+   G  + +
Sbjct: 62  SGLVASGADAYMLHVIPTPGVSYEVVDGGFDCGVMITASHNPYTDNGIKLVNHEGYKMDE 121

Query: 123 EREAIVEE-LFFKEDFDRAKWYEIGEVRREDIIKPYIEAIKSKVDVEAIKKRKPFVVVDT 181
           +   ++E+ +  K +   A    IG     D ++     I S +       +   + +D 
Sbjct: 122 DVLELIEDYIDGKSEVPLATGENIG--CTVDYMQGRNRYIASLISSCGFSLQGMKIGLDC 179

Query: 182 SNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVA 241
           +NG+ S     +   LG +   +N  P+GY    N      +++     V   G D G A
Sbjct: 180 ANGSASSVARPVFDALGAETHVINNAPNGY--NINVACGSTHIEGLQRFVVENGLDIGFA 237

Query: 242 QDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNL----LDDIAKK 297
            DGDADR + +DE G  + GD    L        K G L  +TV  + +         + 
Sbjct: 238 YDGDADRCLAVDERGHLVDGD--LILYVCGTYLNKYGRLAKSTVVPTVMGNFGFFRALEA 295

Query: 298 HGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSG 357
            G    +T VGD  V   + EN   +GGE++G +IF +     DG +T  +++E+     
Sbjct: 296 AGLNYEKTDVGDKYVYACMRENGYNLGGEQSGHIIFGDLAKTGDGILTSLRIMEVLRAER 355

Query: 358 KKFSELIDELPKYYQIKTKRHVEGDRHAIVNK---VAEMARERGYTVDTTDGAKIIFEDG 414
           +K SEL   +  Y Q      V  D+ A++N     A +A+   Y          +  +G
Sbjct: 356 EKLSELTRPVKLYPQQLVNVRV-SDKDAVMNGEDIKAAIAQAEEY----------LEGNG 404

Query: 415 WVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEK 452
            V VRASGTEP++R+ +EA  ++   +   + +  LEK
Sbjct: 405 RVFVRASGTEPLVRVLTEAPDEKLCTKAGAIVLTALEK 442


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: 512
Number of extensions: 26
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: 447
Length adjustment: 33
Effective length of query: 422
Effective length of database: 414
Effective search space:   174708
Effective search space used:   174708
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 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