GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Marivita geojedonensis DPG-138

Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate WP_085636384.1 MGEO_RS08970 phosphoglucosamine mutase

Query= SwissProt::Q976E4
         (455 letters)



>NCBI__GCF_002115805.1:WP_085636384.1
          Length = 447

 Score =  159 bits (401), Expect = 2e-43
 Identities = 139/458 (30%), Positives = 211/458 (46%), Gaps = 38/458 (8%)

Query: 3   KLFGTDGVRGIVNK-ELTPELVLKLSKAIGTFFGKNSK----ILVGRDVRAGGDMLVKIV 57
           KLFGTDGVRG  N   +T ++ L++  A+G  F ++SK    +++G+D R  G M    +
Sbjct: 4   KLFGTDGVRGTANAYPMTADMALRIGAAVGRHFRQDSKGVHRVVIGKDTRQSGYMFENAL 63

Query: 58  EGGLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIR 117
             GL S G+ V   G  PTPA+     ++  D G++I+ASHNPA  NGIK    DG ++ 
Sbjct: 64  TAGLTSTGMNVLLLGPVPTPAVGLLTPSMRADLGIMISASHNPARDNGIKFFGPDGFKLS 123

Query: 118 REKENEIEDLFFTERFNTIEWSSLTT--EVKREDRVISTYVNGILSHVDIEKIKKKNYKV 175
              E EIE L  T     +E +        KR D     Y   + S    + ++    KV
Sbjct: 124 DADEAEIEALIET----GVEPAQAENIGRAKRIDDGRFRYQERVKSTFPAD-LRLDGLKV 178

Query: 176 LIDPANSVGALSTPLVARALGCKI----YTING-NLDPLFSARQPEPTFDSLKETAEVVK 230
           +ID AN     + P V   LG  +     T NG N++    +  P+         A  V 
Sbjct: 179 VIDCANGAAYKAAPEVLWELGADVIPLGVTPNGSNINEGCGSTHPQ-------LAAAAVV 231

Query: 231 TLKVDLGVAHDGDADRAIFIDSEGRVQWGDRSGTLL-SYWASVKNPKAIKKIVTAVSSSS 289
               D+G+  DGDADR I ID  G+V  GD+   L+ + WA  +  +    + T +S+  
Sbjct: 232 AHGADIGICLDGDADRVILIDETGQVADGDQIMALMAARWAEEQRLRDGVLVATVMSNLG 291

Query: 290 LVEEYLSKYNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALM 349
           L E +L    ++++ T VG   +   +       G E++G  +   +    DG M+    
Sbjct: 292 L-ERFLDGRGLRLERTGVGDRYVVEAMRRGGWNLGGEQSGHIVMTDYATTGDGLMAGLQF 350

Query: 350 L-ELLANENVSSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDG 408
           L E+      +SA           +    D  P L+    Y   +    T+SVKA   D 
Sbjct: 351 LGEMCRTGKPASA-----------LARSFDPVPQLLKNVRYDPSVAPLETASVKAAIADA 399

Query: 409 VKIIGKDFWFLVRKSGTEPIIRIMAEAKDENVANNLVN 446
              +      L+RKSGTEP+IR+MAE +DE +   +V+
Sbjct: 400 EARLNGSGRLLIRKSGTEPLIRVMAECEDEALLVEVVD 437


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: 467
Number of extensions: 27
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: 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