GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SynE:Synpcc7942_2132
          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:

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