Alignments for a candidate for pgmA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Shewanella amazonensis SB2B

Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate 6937015 Sama_1189 phosphoglucomutase/phosphomannomutase family protein (RefSeq)

Query= SwissProt::P18159
         (581 letters)



>FitnessBrowser__SB2B:6937015
          Length = 585

 Score =  313 bits (801), Expect = 2e-89
 Identities = 207/555 (37%), Positives = 292/555 (52%), Gaps = 25/555 (4%)

Query: 29  GDEQALEDCFYKDLEFGTGGMRGEIGAGTNRMNIYTVRKASAGFAAYISKQGEEAKKRGV 88
           GD++ALE  F   L FGT G+RG +G G   MN   VR+ SAG  AY+  Q ++AK+RG+
Sbjct: 32  GDDRALEAAFDGRLAFGTAGIRGIVGPGPMGMNRLLVRETSAGLGAYLEAQIKDAKRRGL 91

Query: 89  VIAYDSRHKSPEFAMEAAKTLATQGIQTYVFDELRPTPELSFAVRQLNAYGGIVVTASHN 148
           VI +D RH S  FA +AA  L+  G +  +   + PTP ++F V+   A  GIVVTASHN
Sbjct: 92  VIGFDGRHDSRVFAHDAACVLSAMGFKVRLTSHVAPTPLVAFGVKHFEAAAGIVVTASHN 151

Query: 149 PPEYNGYKVYGDDGGQ-LPPKEADIVIEQVNAIENELTITVDEENKLKEKGLIKIIGEDI 207
           PP+YNGYKVY ++G Q +PP +A I      A   EL    + E    ++G +  + +D 
Sbjct: 152 PPKYNGYKVYWENGAQIIPPHDAGIAACIDRAANLELPWMPEPE--AVKQGRLSFLQDDF 209

Query: 208 DKVYTEK-LTSISVHP---ELSEEVDVKVVFTPLHGTANKPVRRGLEALGYKNVTVVKEQ 263
            + Y    L S  +HP     +    + + +T +HG       R L   G+  V  V  Q
Sbjct: 210 FERYRRAILHSPLLHPAGESQAGRASLGIAYTAMHGVGAPMAERVLRDAGFSQVYSVAAQ 269

Query: 264 ELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILIATDPDADRLGIAVKNDQGKYTVL 323
             PD NF TV  PNPEE  A +  I    ++ A +  A DPDADR  +A +   G Y +L
Sbjct: 270 REPDGNFPTVNFPNPEEPGAMDMVIAEAGDKGALLACANDPDADRFALAARQSDGGYRML 329

Query: 324 TGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIGRAVASSFGLDTIDTLTGFKFI 383
           +G+QTGALL  YLLS  +  G+     +V  TIV+S +  A+A+ +G  +  TLTGFK++
Sbjct: 330 SGDQTGALLCDYLLSHWQGAGV----PLVGNTIVSSALLHAIAAHYGAHSYTTLTGFKWL 385

Query: 384 GEKIKEYEASGQYTFQFGYEESYGYLIGDFARDKDAIQAALLAVEVCAFYKKQGMSLYEA 443
               ++ E + Q  F F YEE+ GY +G+   DKD I A L    + A    +G  ++ A
Sbjct: 386 MNTAQQLE-TPQQPFLFAYEEALGYTVGNLVWDKDGISAQLCFANLAAELLAEGKDVWAA 444

Query: 444 LINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFRQNPPQKMAGKQVVTAEDYAVSKR 503
           L  L+  +G Y     S+ L   +G   I A L   R NPP ++  + VV  ED     R
Sbjct: 445 LERLYRRHGLYVNRQVSIAL--GEGTPDIGAWL---RDNPPTEIDKRPVVAREDLK-RLR 498

Query: 504 TLLTESKEEAIDLPKSNVLKYFL-----EDGSW--FCLRPSGTEPKVKFYFAVKGSSLED 556
            +  + +EE I LP S+VL Y L       GS     +RPSGTEPK+K Y+ +     +D
Sbjct: 499 KVYADGREEEIALPASDVLIYHLGASDATPGSTARVIVRPSGTEPKIKCYYELVLPMADD 558

Query: 557 SEKRLAVLSEDVMKT 571
                A L  D + T
Sbjct: 559 IAMADAQLQGDALMT 573


Lambda     K      H
   0.313    0.133    0.371 

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: 766
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: 581
Length of database: 585
Length adjustment: 36
Effective length of query: 545
Effective length of database: 549
Effective search space:   299205
Effective search space used:   299205
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources