GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Shewanella amazonensis SB2B

Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate 6938122 Sama_2243 phosphoglucosamine mutase (RefSeq)

Query= SwissProt::Q976E4
         (455 letters)



>FitnessBrowser__SB2B:6938122
          Length = 452

 Score =  167 bits (423), Expect = 6e-46
 Identities = 133/450 (29%), Positives = 204/450 (45%), Gaps = 27/450 (6%)

Query: 3   KLFGTDGVRGIVNK-ELTPELVLKLSKAIGTFFGKNS--KILVGRDVRAGGDMLVKIVEG 59
           K FGTDGVRG V +  +TP+  +KL  A GT    +   ++++G+D R  G ML   +E 
Sbjct: 4   KYFGTDGVRGKVGEFPITPDFAMKLGWAAGTVMAASGTKEVIIGKDTRLSGYMLESAMEA 63

Query: 60  GLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIRRE 119
           G  + GV V   G  PTPA+ Y   T   D GVVI+ASHNP   NGIK     G ++  E
Sbjct: 64  GFCAAGVNVALTGPLPTPAIAYLTSTFRADAGVVISASHNPYYDNGIKFFSNTGTKLTDE 123

Query: 120 KENEIEDLFFTERFNTIEWSSLTT-------EVKREDRVISTYVNGILSHVDIEKIKKKN 172
           +E EIE L      + IE  ++T        +V+R +     Y+           +    
Sbjct: 124 QELEIERLL----VSAIEGGAMTCVASDKLGKVRRINDAAGRYIE-FCKGTFPNSLSLTG 178

Query: 173 YKVLIDPANSVGALSTPLVARALGCKIYTINGNLDPLFSARQPEPTFDSLKETAEVVKTL 232
            K+++D A+         V R LG ++ +IN   D +        T     +TA ++   
Sbjct: 179 LKIVVDSAHGAAYHIAKNVYRELGAEVISINDKPDGININEHCGATHMDSLQTAVMIH-- 236

Query: 233 KVDLGVAHDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKKIVTAVSSSSLVE 292
           + DLG+A DGDADR + +DS+G+V  GD    LL+  A  +  + +  ++  + S+   E
Sbjct: 237 EADLGIALDGDADRLMMVDSKGQVIDGDALLYLLAKSAQQRG-EQVSGVIGTLMSNLGFE 295

Query: 293 EYLSKYNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALMLEL 352
           + L+   I     KVG   +   + +     G E +G  +        D  ++   +L  
Sbjct: 296 QALANLGIPFKRAKVGDRYVVELLKETGWRLGGENSGHLLMLDFTTTGDAIVASLQVLRA 355

Query: 353 LANENVSSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDGVKII 412
           L       A+    L  +  V   V L     V   +  + +  +T+            +
Sbjct: 356 LLESGAGLADAITELNMFPQVLINVRLNGNAAVGLSHPSVSDAVATAE---------SAL 406

Query: 413 GKDFWFLVRKSGTEPIIRIMAEAKDENVAN 442
           G D   L+RKSGTEP+IR+M EAKD   AN
Sbjct: 407 GNDGRVLLRKSGTEPLIRVMVEAKDAVKAN 436


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: 415
Number of extensions: 19
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: 452
Length adjustment: 33
Effective length of query: 422
Effective length of database: 419
Effective search space:   176818
Effective search space used:   176818
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