GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoB 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)



>lcl|FitnessBrowser__MR1:200919 SO1755
           phosphoglucomutase/phosphomannomutase family protein
           (NCBI ptt file)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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