GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Pedobacter sp. GW460-11-11-14-LB5

Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate CA265_RS13185 CA265_RS13185 phosphoglucosamine mutase

Query= SwissProt::Q976E4
         (455 letters)



>FitnessBrowser__Pedo557:CA265_RS13185
          Length = 461

 Score =  224 bits (572), Expect = 3e-63
 Identities = 143/450 (31%), Positives = 241/450 (53%), Gaps = 17/450 (3%)

Query: 9   GVRGIVNKE----LTPELVLKLSKAIGTFFGK---NSKILVGRDVRAGGDMLVKIVEGGL 61
           G+RG +       LTP  ++K + A G++  +   N +I++GRD R  G+M+  +V G L
Sbjct: 9   GIRGTIGGRAGDGLTPFDIVKFTAAFGSWVVQKTGNKRIVLGRDARISGEMVNNLVIGTL 68

Query: 62  LSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIRREKE 121
             +G+EV D G++ TP ++ AV      GG+++TASHNP  +N +K+++  G  I     
Sbjct: 69  QGLGIEVIDLGLSTTPTVEVAVPDEKAGGGIILTASHNPKQWNALKLLNASGEFISDADG 128

Query: 122 NEIEDLFFTERFNTIEWSSLTTEVKREDRVISTYVNGILS--HVDIEKIKKKNYKVLIDP 179
            E+ DL  +  F+  +   L   +K  D  +  +++ +L+   VD+E IKK ++KV+ID 
Sbjct: 129 KEVLDLAESADFDFADVDKLGKVIK-NDTYLQKHIDKVLALPLVDVEAIKKADFKVVIDC 187

Query: 180 ANSVGALSTPLVARALG-CKIYTINGNLDPLFSARQPEPTFDSLKETAEVVKTLKVDLGV 238
            NS G +  P + +ALG  K+  +    D  F    PEP  ++L E ++ V+    DLG+
Sbjct: 188 VNSTGGIFIPALLKALGVSKVVELYCTPDGHF-PHNPEPLPENLTEISKEVQKQNADLGI 246

Query: 239 AHDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKKIVTAVSSSSLVEEYLSKY 298
             D D DR  F++ +G +   + +   ++ +     P      V+ +SS+  + +     
Sbjct: 247 VVDPDVDRLCFVNEDGSMFGEEYTLVAVADYVLKNTP---GNTVSNLSSTRALRDVTESA 303

Query: 299 NIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALMLELLANENV 358
             + + + VG V++ +K+   NA+ G E NGG +YP   Y RD  +  AL L  LA    
Sbjct: 304 GAEYNASAVGEVNVVNKMKATNAIIGGEGNGGIIYPESHYGRDALVGIALFLTHLAKFGK 363

Query: 359 SSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDGVKIIGKDFWF 418
           S + L    P+Y++ K K+ L P + ++ + K++ E Y        TIDG+KI     W 
Sbjct: 364 SISVLRSSYPQYHISKNKITLTPEMDIDNLLKQVEEKYKNQPYS--TIDGLKIEFDKTWV 421

Query: 419 LVRKSGTEPIIRIMAEAKDENVANNLVNEL 448
            +R+S TEPIIRI +EA++E +A NL N++
Sbjct: 422 HLRRSNTEPIIRIYSEAENETIAENLANKI 451


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: 490
Number of extensions: 29
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 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