GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Chryseobacterium viscerum 687B-08

Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate WP_103231575.1 C1634_RS03120 phosphoglucosamine mutase

Query= SwissProt::Q976E4
         (455 letters)



>NCBI__GCF_002899945.2:WP_103231575.1
          Length = 460

 Score =  240 bits (613), Expect = 6e-68
 Identities = 160/462 (34%), Positives = 242/462 (52%), Gaps = 24/462 (5%)

Query: 1   MGKLFGTDGVRGI----VNKELTPELVLKLSKAIGTFF--GKNSK---ILVGRDVRAGGD 51
           M  +    G+RG     VN  LTP  V+K + A GT+    KN K   +++GRD R  G 
Sbjct: 1   MSLIKSISGIRGTIGGKVNDNLTPLDVVKFASAFGTWLQNNKNKKDLTLIIGRDARISGQ 60

Query: 52  MLVKIVEGGLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDK 111
           M+  +V   L  +G+ V D G++ TP ++  V  L  DGG+++TASHNP  +N +K++++
Sbjct: 61  MVSSLVTATLQGLGINVVDLGLSTTPTVEIMVPELNADGGIILTASHNPKQWNALKLLNE 120

Query: 112 DGIEIRREKENEIEDLFFTERFNTIEWSSLTTEVKREDRVISTYVNGILS--HVDIEKIK 169
            G  I  E   E+  L  +E FN  E   L     RED     ++  IL    VD E IK
Sbjct: 121 KGEFITGENGAEVLALAESEDFNYAEVDDLGQYETRED-AFDIHIKQILDLPMVDAEAIK 179

Query: 170 KKNYKVLIDPANSVGALSTPLVARALGCKIYTINGNLDPL-FSARQPEPTFDSLKETAEV 228
            KN+KV++D  NS G ++ P++   LGC+  T+    +P       PEP  + L +  E+
Sbjct: 180 AKNFKVVLDAVNSTGGIAIPMLLDTLGCE--TVKLYCEPTGHFPHNPEPLKEHLGDICEL 237

Query: 229 VKTLKVDLGVAHDGDADRAIFIDSEGRVQWGDRSG--TLLSYWASVKNPKAIKKIVTAVS 286
           VK    DLG+  D D DR   ID +G + +G+      +  Y    KN  A+  +    S
Sbjct: 238 VKKENADLGIVVDPDVDRLALIDEKGEM-FGEEYTLVAVADYLLKHKNGVAVSNL----S 292

Query: 287 SSSLVEEYLSKYNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSF 346
           SS  + +    +N +   + VG V++   + ++NA+ G E NGG +YP   Y RD  +  
Sbjct: 293 SSRALRDVAHTHNSEYFASAVGEVNVVTLMKEKNAVIGGEGNGGIIYPDLHYGRDSLVGV 352

Query: 347 ALMLELLANENVSSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITI 406
           AL L  LA EN + +EL    P Y++ K K++L P + V+ I  K+ + Y    V    +
Sbjct: 353 ALFLTHLAKENKTVSELRAGYPSYFMGKKKIELTPEIDVDAILSKMEQEYKNEEVS--VV 410

Query: 407 DGVKIIGKDFWFLVRKSGTEPIIRIMAEAKDENVANNLVNEL 448
           DGVKI  ++ W  +RKS TEPIIRI  EAK +  A+ L +++
Sbjct: 411 DGVKIDFENNWVHLRKSNTEPIIRIYTEAKSQEEADKLGDDI 452


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: 469
Number of extensions: 22
Number of successful extensions: 6
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: 460
Length adjustment: 33
Effective length of query: 422
Effective length of database: 427
Effective search space:   180194
Effective search space used:   180194
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