GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Erythrobacter gangjinensis K7-2

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2); phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_047006996.1 AAW01_RS08900 phosphomannomutase/phosphoglucomutase

Query= BRENDA::M1T754
         (460 letters)



>NCBI__GCF_001010925.1:WP_047006996.1
          Length = 472

 Score =  632 bits (1630), Expect = 0.0
 Identities = 316/472 (66%), Positives = 362/472 (76%), Gaps = 12/472 (2%)

Query: 1   MSHKFDPTTLREYDIRGIVGKTLNPADATAIGRGFGTLLRRAGGTRA-----AVGYDGRH 55
           MSH FDPTTLREYDIRGI+G+TL P DA AIGRGF TLL R G         AVGYDGR 
Sbjct: 1   MSHIFDPTTLREYDIRGIIGETLGPDDARAIGRGFATLLLREGSVEGRRPCVAVGYDGRV 60

Query: 56  SSPLLEAALVQGLIASGIDVVRVGLGPTPMLYYAEAVLE-VDGGIMITGSHNPPDYNGFK 114
           SSP+LE AL++GL + G  V R+G+  TPMLYYAEA  E VDGGI ITGSHNP +YNGFK
Sbjct: 61  SSPMLEHALIEGLTSGGCAVRRIGMSATPMLYYAEASAEEVDGGIQITGSHNPANYNGFK 120

Query: 115 MVFQHRPFFGEDILKIGTMAAEGDWEEGEGTVTNADIMDMYVDRLIAGYQG------GAF 168
           MVF+ RPFFG DI ++G +AA GDW  G G V + DI++ YV+RL+    G         
Sbjct: 121 MVFEGRPFFGGDIQRLGELAAAGDWTSGMGEVDSVDIIEQYVERLLTALSGIDEGVLSGL 180

Query: 169 KVAWDAGNGAAGPVIEKLVKFLPGEHHLLYTDVDGDFPNHHPDPTEEKNLVDLKALVAEK 228
           ++ WDAGNGAAGP +E L + LPGEHHLLYT+VDG+FPNHHPDPT E NLVDL+ALVA K
Sbjct: 181 RIGWDAGNGAAGPALELLTQRLPGEHHLLYTEVDGNFPNHHPDPTVEANLVDLRALVAAK 240

Query: 229 GLDFGIGFDGDGDRIGAIDGKGRVVWGDQLLGILAEPVLKAVPGGTIIADVKTSQALYDR 288
            LDFG+ FDGDGDRIGAIDG+GRVVWGDQLL I AE +L  +P  T+IADVK S+AL+D 
Sbjct: 241 NLDFGVAFDGDGDRIGAIDGEGRVVWGDQLLMIYAEDLLGRLPNATVIADVKASRALFDH 300

Query: 289 VAELGGKPLMWKTGHSLIKAKMKEVDSPLGGEMSGHIFFAWDYYGFDDAIYAAVRLMGAV 348
           VA  GGKP+MWKTGHSLIK+KMKEV SPL GEMSGH+FFA DYYGFDDA+YAAVRLM A 
Sbjct: 301 VAAHGGKPVMWKTGHSLIKSKMKEVSSPLAGEMSGHVFFADDYYGFDDALYAAVRLMAAS 360

Query: 349 RHSGKSLTELKDAMPAMVNTPEMRFQVDESRKFAVIEEVLQRLEADGADINRTDGARVNT 408
              G+S+TEL+ AMP M+NTPEMRFQVDESRKFA IEE+  R+ A  A  + TDG RV T
Sbjct: 361 ARLGRSVTELRGAMPEMINTPEMRFQVDESRKFAAIEEIAARIAASDAVADTTDGVRVTT 420

Query: 409 PDGWWLLRASNTQDVLVARAEAKDEAGLERLLKQIDTQLELSHIARGEQAGH 460
            DGWWLLRASNTQDVLVARAE+  + GLERLL  ID QL LS + RG   GH
Sbjct: 421 DDGWWLLRASNTQDVLVARAESDTQEGLERLLASIDEQLALSGLERGSNVGH 472


Lambda     K      H
   0.318    0.139    0.417 

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: 730
Number of extensions: 36
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: 460
Length of database: 472
Length adjustment: 33
Effective length of query: 427
Effective length of database: 439
Effective search space:   187453
Effective search space used:   187453
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 (21.7 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