GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pgmA in Synechococcus elongatus PCC 7942

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate Synpcc7942_2132 Synpcc7942_2132 phosphoglucosamine mutase

Query= SwissProt::Q68BJ6
         (456 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_2132 Synpcc7942_2132
           phosphoglucosamine mutase
          Length = 472

 Score =  211 bits (536), Expect = 5e-59
 Identities = 146/461 (31%), Positives = 233/461 (50%), Gaps = 25/461 (5%)

Query: 4   LFGTFGVRGIANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDALIS 63
           LFGT G+RG   E +T   A ++G   G +L++ G +R  VVVG+D+R S  ML  AL S
Sbjct: 26  LFGTDGIRGRVGEHLTAPLAQQVGFWTGQVLRQAGGDRGPVVVGQDSRNSSNMLAMALSS 85

Query: 64  GLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123
           GL + G +V+ +G+ PTP + + T+H  A GG +I+ASHNPP  NGIK+   +G  L ++
Sbjct: 86  GLAAAGVEVLHLGLCPTPGVAYLTHHSEAIGGVMISASHNPPGDNGIKVFGADGSKLDRQ 145

Query: 124 REAIVEELFFSE--DFHRAKWNEIGELRKEDIIKPYIEAIK----NRVDVEAIKKRRPFV 177
            +A +E     +        W +     +  +   Y  AI      R +++ +K     +
Sbjct: 146 LQAAIEAGLRGQQTSLPATTWGQ--HYYQPQLADHYQAAIAQSLGQRANLQGLK-----I 198

Query: 178 VVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGAD 237
           V+D + GA +L  P L RELG +V++++  PDG+    N      +L      V   GAD
Sbjct: 199 VLDLAWGAAALLAPRLFRELGAEVIALHDLPDGN--QINVNCGSTHLARLQAAVLEQGAD 256

Query: 238 FGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLREN--GGGLLVTTIATSNLLDDIA 295
            G A DGDADR + +D  GR + GD    L    + ++    G  +VTT+  +   +   
Sbjct: 257 MGFAFDGDADRVLAVDGRGRSVDGDHILFLWGRELEQQQQLPGQAIVTTVMANLGFERAW 316

Query: 296 KRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAK 355
           +  G + +RT VGD  V   +      +GGE++G ++   + L  DG +T A +  +   
Sbjct: 317 QAVGGEFVRTAVGDQYVQAEMQARGAMLGGEQSGHILCRHYALTGDGTLTAAHVAALVQA 376

Query: 356 SGKKFSELIDELPKYYQ--FKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFDD 413
           SG   ++L+D+  + Y    +  R  + DR+      A L +        TD    + D 
Sbjct: 377 SGVSLADLVDQSFRPYPQLLRNVRVEDRDRRCNWQNCAALTQ--AIAAAETD----MGDR 430

Query: 414 GWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEAL 454
           G VLVRASGTEP++RI  EA+  ++   +    +++ E  L
Sbjct: 431 GRVLVRASGTEPLLRIMVEAEEAQQVEHWTTHLVQVAESHL 471


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: 466
Number of extensions: 24
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: 456
Length of database: 472
Length adjustment: 33
Effective length of query: 423
Effective length of database: 439
Effective search space:   185697
Effective search space used:   185697
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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