GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Shewanella oneidensis MR-1

Align Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphoglucomutase-1; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized)
to candidate 200919 SO1755 phosphoglucomutase/phosphomannomutase family protein (NCBI ptt file)

Query= SwissProt::Q7TSV4
         (620 letters)



>FitnessBrowser__MR1:200919
          Length = 573

 Score =  333 bits (853), Expect = 2e-95
 Identities = 211/570 (37%), Positives = 297/570 (52%), Gaps = 33/570 (5%)

Query: 19  MDARLDQETAQWLRWDQNPLTSESVKQLIAGGNKEELRKCFGARMEFGTAGLRAPMGAGI 78
           M+  L  +   WL+ D +P T   ++ LI  GN+ EL   F  R+EFGTAGLR  +GAG 
Sbjct: 1   MNTHLQLQIQHWLKNDPDPSTQAQLQALIDSGNEAELAARFAGRLEFGTAGLRGVVGAGP 60

Query: 79  SRMNDLTIIQTTQGFCRYLEKQFSDLKQRGVVISFDARAHPASGGSSRRFARLAATAFIT 138
             MN L I QT+ G   YL +Q  D+ +RGVVI +D R        S  FA   A+    
Sbjct: 61  MGMNRLVIRQTSAGLGAYLLEQIHDVAERGVVIGYDGRH------DSYTFAHDTASVLTA 114

Query: 139 QGVPVYLFSDITPTPFVPYTVSHLKLCAGIMITASHNPKQDNGYKVYWDNGAQIISPHDR 198
            G+ V L + + PTP V + V H    AGI++TASHNP Q NGYKVYW+NGAQII PHD 
Sbjct: 115 MGIKVRLTAKVAPTPLVAFGVKHFNAAAGIVVTASHNPPQYNGYKVYWENGAQIIPPHDS 174

Query: 199 GISQAIEE-NLEPWPQAWEESLVDSSPLLHNPSASIGNDYFEDLKKYCFHRTV----NKE 253
           GI+  IE+   +  P    +  +    L+      + +DY+E  ++   H  V       
Sbjct: 175 GIAAKIEQAATQAIPFMELDDAIKQGKLIW-----LNDDYYETYRRGVMHAKVLQNHTAP 229

Query: 254 SKVKFVHTSVHGVGHEFVQLAFKAFDLAPPEAVPQQKDPDPEFPTVKYPNPEEGKGVLTL 313
            KV   +T++HGVG +  +   K        +V  Q++PD +FPTV +PNPEE KG + L
Sbjct: 230 EKVSLAYTAMHGVGADMAETVLKDAGFTQVYSVAAQREPDGDFPTVNFPNPEE-KGAMDL 288

Query: 314 SFALADKIKAKIVLANDPDADRLAVAEKQDSGEWRVFSGNELGALLGWWLFTSWKEKNQD 373
             A A K  A +  ANDPDADR AVA ++D GE+++ +G+++G L G +L +     + D
Sbjct: 289 VIAEAKKHSAMLACANDPDADRFAVAVRKDDGEYQMLTGDQVGVLFGHYLLS---HASAD 345

Query: 374 QSNLKDTYMLSSTVSSKILRAIALKEGFHFEETLTGFKWMGNRAQQLGDQGKTVLFAFEE 433
           Q  L  T ++SS++ SKI        G     TLTGFKW+ N            LFA+EE
Sbjct: 346 Q-RLVGTTIVSSSLLSKIANGF----GVESYTTLTGFKWLMNVGIAQSQPDNQFLFAYEE 400

Query: 434 AIGYMCCPFVLDKDGVSAAVICAELASFLATKNLSLSQQLNAIYVEYGYHITTASYFICH 493
           A+GY     V DKDG+SA V  A+L + LA K  ++  +L  IY E G+H+   +     
Sbjct: 401 ALGYTVGNMVWDKDGLSALVAFAQLTAELAAKGQTIWDRLEQIYREQGFHLNAQASIALK 460

Query: 494 DQGTIQNLFGNLRNYDGKNNYPKMCGKFEISAIRDLTTGYDDSQPDKKAVLPTSKSSQMI 553
            +    N+   LR +      P   G+  + +  DL         D K       +S ++
Sbjct: 461 PE--TPNIGAYLREHP-----PLTIGEHAVVSTDDL-KALSRRFADGKVENINLPASDVL 512

Query: 554 TFTFANGGVATMRTSGTEPKIKYYAELCAP 583
           T+  +NG    +R SGTEPKIK Y E+  P
Sbjct: 513 TYRLSNGARVIVRPSGTEPKIKCYYEVVEP 542


Lambda     K      H
   0.317    0.133    0.403 

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: 887
Number of extensions: 42
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: 620
Length of database: 573
Length adjustment: 37
Effective length of query: 583
Effective length of database: 536
Effective search space:   312488
Effective search space used:   312488
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: 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