GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Sphingomonas koreensis DSMZ 15582

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate Ga0059261_1954 Ga0059261_1954 phosphoglucosamine mutase (EC 5.4.2.10)

Query= SwissProt::Q68BJ6
         (456 letters)



>FitnessBrowser__Korea:Ga0059261_1954
          Length = 461

 Score =  224 bits (572), Expect = 3e-63
 Identities = 159/443 (35%), Positives = 231/443 (52%), Gaps = 32/443 (7%)

Query: 3   KLFGTFGVRGIAN-EEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61
           K FGT G+RG  N   +T   A+++GMA G   +R G  +  VV+G+DTR+SG M+++AL
Sbjct: 19  KYFGTDGIRGKTNVTPMTAAMAMQVGMAAGAHFRR-GDHKHRVVIGKDTRLSGYMIENAL 77

Query: 62  ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
           ++G  S G DV+ VG  PTPA+   T+   AD G +I+ASHNP   NGIKL  P+G  L 
Sbjct: 78  VAGFTSVGMDVVLVGPMPTPAVAMLTHSMRADMGVMISASHNPYADNGIKLFGPDGYKLS 137

Query: 122 KEREAIVEELFFSEDFHRAKWNEIGELRK-EDIIKPYIEAIKNRVDVEAIKKRRPFVVVD 180
              E  +E L   E    A   +IG  ++ ED    YI   K+    E ++     VVVD
Sbjct: 138 DADELAIEALIDGE-IPLAPAADIGRAKRIEDAKGRYIHFAKSTFP-EDLRLDGLKVVVD 195

Query: 181 TSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFGV 240
            +NGA     P  L ELG +VV++   PDG     N +          E V A GA  G+
Sbjct: 196 CANGAAYQVAPSALWELGAEVVAIGVTPDG--KNINDQVGSTAPLTLCETVVASGAHIGI 253

Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVLRE---NGGGLLVTTIATSNLLDDIAKR 297
           A DGDADR + +DE G  + GD+  A +A    R+   +GGGL+ T ++   L   +A +
Sbjct: 254 ALDGDADRLIVVDEQGEVVDGDQLMATIASGWARQGRLSGGGLVATVMSNLGLERHLAAQ 313

Query: 298 NGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSG 357
            G  ++RTKVGD  V   +  +   +GGE++G +I  D+    DG +   +++    ++G
Sbjct: 314 -GLGLVRTKVGDRYVLEKMRASGYNVGGEQSGHIILSDYATTGDGLVAALQVLAELVRAG 372

Query: 358 KKFSELI---DELP---KYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIF 411
              SE++   D LP   K  +F   + +E +    V   AE            DGT    
Sbjct: 373 APASEVLHRFDPLPQLLKNVRFSGGKPLENETVKSVIAAAE---------TELDGT---- 419

Query: 412 DDGWVLVRASGTEPIIRIFSEAK 434
             G VL+RASGTEP+IR+ +E +
Sbjct: 420 --GRVLIRASGTEPVIRVMAEGE 440


Lambda     K      H
   0.317    0.139    0.396 

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: 548
Number of extensions: 35
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: 456
Length of database: 461
Length adjustment: 33
Effective length of query: 423
Effective length of database: 428
Effective search space:   181044
Effective search space used:   181044
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