GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Roseivirga spongicola UST030701-084

Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate WP_068216838.1 AWW68_RS04035 phosphoglucosamine mutase

Query= SwissProt::Q976E4
         (455 letters)



>NCBI__GCF_001592965.1:WP_068216838.1
          Length = 461

 Score =  219 bits (559), Expect = 1e-61
 Identities = 144/459 (31%), Positives = 246/459 (53%), Gaps = 29/459 (6%)

Query: 10  VRGIVNKELTPELVLKLSKAIGTFF----GKNSKILVGRDVRAGGDMLVKIVEGGLLSVG 65
           + G V + LTP   +K + A G++     GK  KI++GRD R  G M+  +V   L+ +G
Sbjct: 14  IGGAVGESLTPVDAVKFAAAFGSWVVAKTGKK-KIIIGRDARPSGQMISDLVSSTLIGLG 72

Query: 66  VEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIRREKENEIE 125
           ++V D G++ TP ++ AV      GG+++TASHNP  +N +K+++  G  I  +   E+ 
Sbjct: 73  IDVVDLGLSTTPTVEIAVPLEEAGGGIILTASHNPVQWNALKLLNDKGEFISGDDGKEVL 132

Query: 126 DLFFTERFNTIEWSSLTTEVKREDRVISTYVNGILS--HVDIEKIKKKNYKVLIDPANSV 183
           ++   + F   +   L  +V   D  I  ++  +L+   VD+E IKK  +K+++D  NS 
Sbjct: 133 EIAEKDNFKFADVKKL-GKVTTNDSYIQKHIEMVLALPLVDVEAIKKAKFKIVVDAVNST 191

Query: 184 GALSTPLVARALGCKIYTINGNLDPLFS------ARQPEPTFDSLKETAEVVKTLKVDLG 237
           G +S   + +ALG +       ++PL+          PEP  + L + + ++++ K DLG
Sbjct: 192 GGISVLPLLKALGVE------TVEPLYCEPNGQFPHNPEPLPEHLGQISSMLESGKYDLG 245

Query: 238 VAHDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKKIVTAVSSSSLVEEYLSK 297
           +  D D DR  F+D  G V +G+   TL++  A     +     V+ +SS+  + +   K
Sbjct: 246 IVVDPDVDRLAFVDESGSV-FGEEY-TLVAV-ADYVLSQTKGNTVSNLSSTRALRDVTEK 302

Query: 298 YNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALMLELLANEN 357
           Y  Q + + VG V++  K+ +  A+ G E NGG +YP   Y RD  +  AL L  LA   
Sbjct: 303 YGCQYEPSAVGEVNVVVKMKEIGAVIGGEGNGGIIYPELHYGRDALVGIALFLTHLAKFG 362

Query: 358 VSSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDGVKIIGKDFW 417
              + L  + P Y++ K K++L P + V+++  K+ E Y    +   T+DGVKI     W
Sbjct: 363 KRVSMLRAKYPSYHISKNKIELSPEIDVDKVLTKMKEQYKKQPIN--TVDGVKIEFDKEW 420

Query: 418 FLVRKSGTEPIIRIMAEAKD----ENVANNLVNELKKIV 452
             +RKS TEPIIRI AE++     E++A  +++++++IV
Sbjct: 421 VHLRKSNTEPIIRIYAESESAATAEHLAQKIMSDIREIV 459


Lambda     K      H
   0.316    0.136    0.384 

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: 472
Number of extensions: 17
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: 461
Length adjustment: 33
Effective length of query: 422
Effective length of database: 428
Effective search space:   180616
Effective search space used:   180616
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