GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Caldicellulosiruptor kronotskyensis 2002

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_013429174.1 CALKRO_RS00500 phosphoglucomutase/phosphomannomutase family protein

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



>NCBI__GCF_000166775.1:WP_013429174.1
          Length = 471

 Score =  234 bits (597), Expect = 5e-66
 Identities = 159/467 (34%), Positives = 228/467 (48%), Gaps = 23/467 (4%)

Query: 5   FGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALISG 64
           FGT G R I  +  T E   K+  A    +K +G     +V+G D R   +         
Sbjct: 4   FGTGGWRAIIGDDFTKENIQKVAQAVSIYMKEKGIDSDGIVLGYDRRFLSDKAARWFSEV 63

Query: 65  LLSVGCDVIDVG-IAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123
           L + G  V  +  +APTP V +  K  N   GA +TASHNP +YNGIKL    G     E
Sbjct: 64  LSANGIKVFFINKVAPTPLVMFTVKKLNTKFGATVTASHNPADYNGIKLFIEEGRDAPFE 123

Query: 124 REAIVEEL---FFKEDFDRAKWYEIGEVRREDIIKP---YIEAIKSKVDVEAIKKRKPFV 177
             + +E +      +   R K+ +  E    +II P   YI+AI S +D+EAIKKRK  +
Sbjct: 124 VTSEIETIANSLLSDSIKRLKFEKAIENGWIEIIDPFDDYIDAILSMIDIEAIKKRKLRI 183

Query: 178 VVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGAD 237
           ++D   G    +L  +L    C V T++ + D  F  R P P    L     +V   G D
Sbjct: 184 LLDPMYGVSRTSLQTILITARCDVDTIHERHDTLFGGRLPSPTTSTLYRLKHLVVEKGYD 243

Query: 238 FGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKG-GGLLVTTVATSNLLDDIAK 296
            G+  DGDADR   IDE G FI  +    L+    LK KG  G +V  +AT++LLD IA 
Sbjct: 244 LGIGTDGDADRVGIIDEIGNFIHPNDILVLLYYYFLKYKGWKGPVVRNLATTHLLDRIAS 303

Query: 297 KHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKS 356
             G K     VG   ++  + E    IGGE +GG+    H+ G+DG      +VE+  K+
Sbjct: 304 SFGEKCYEVPVGFKYISAKMEETGAIIGGESSGGLTIKGHIKGKDGIFAATLLVELICKT 363

Query: 357 GKKFSELIDELPKYYQIKTKRHVEGD---RHAIVNKVAEMARERGY---------TVDTT 404
           G+K SE+++E+ + Y I     VE D         K+ E+  ++ +          V   
Sbjct: 364 GRKLSEILEEIHRIYGILYM--VENDFSFEPEEKEKIWEILFDKKHLPDFPFEISNVSYI 421

Query: 405 DGAKIIFED-GWVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIELL 450
           DG K+ F++ GWVL R SGTEP++RI+SE + K  A+E   +  E L
Sbjct: 422 DGVKVYFKNGGWVLARFSGTEPLLRIYSEMEEKVHAEEVCKIFAEFL 468


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: 585
Number of extensions: 34
Number of successful extensions: 4
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: 471
Length adjustment: 33
Effective length of query: 422
Effective length of database: 438
Effective search space:   184836
Effective search space used:   184836
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