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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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