GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Shewanella sp. ANA-3

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 7025556 Shewana3_2707 phosphoglucomutase/phosphomannomutase alpha/beta/subunit (RefSeq)

Query= SwissProt::Q7TSV4
         (620 letters)



>FitnessBrowser__ANA3:7025556
          Length = 573

 Score =  336 bits (861), Expect = 2e-96
 Identities = 216/576 (37%), Positives = 299/576 (51%), Gaps = 45/576 (7%)

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

Query: 79  SRMNDLTIIQTTQGFCRYLEKQFSDLKQRGVVISFDARAHPASGGSSRRFARLAATAFIT 138
             MN L I QT+ G   YL +Q  D  +RGVVI +D R        SR FA   A+    
Sbjct: 61  MGMNRLVIRQTSAGLGAYLLEQIKDAAERGVVIGYDGRH------DSRTFAHDTASVLTA 114

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

Query: 199 GISQAIEENLEPWPQAWEESLVDSSPLLHNPSAS-------IGNDYFEDLKKYCFHRTVN 251
           GI+  I           E +   + P +    A+       + +DY+E  ++   H  V 
Sbjct: 175 GIAAKI-----------ELAATQAIPFMDQVEATKQGKLIWLQDDYYETYRRGVMHANVL 223

Query: 252 KES----KVKFVHTSVHGVGHEFVQLAFKAFDLAPPEAVPQQKDPDPEFPTVKYPNPEEG 307
           + +    KV   +T++HGVG E  +   K    A   +V  Q++PD +FPTV +PNPEE 
Sbjct: 224 QNNTAPEKVSLAYTAMHGVGAEMAETVLKDAGFAQVYSVVAQREPDGDFPTVNFPNPEE- 282

Query: 308 KGVLTLSFALADKIKAKIVLANDPDADRLAVAEKQDSGEWRVFSGNELGALLGWWLFTSW 367
           KG + L  A A K  A +  ANDPDADR AVA ++D GE+++ +G+++G L G +L +  
Sbjct: 283 KGAMDLVIAEAKKHGAMLACANDPDADRFAVAVRKDDGEYQMLTGDQVGVLFGHYLLSHA 342

Query: 368 KEKNQDQSNLKDTYMLSSTVSSKILRAIALKEGFHFEETLTGFKWMGNRAQQLGDQGKTV 427
            +    +  L  T ++SS++ SKI +      G     TLTGFKW+ N            
Sbjct: 343 SK----EQRLVGTTIVSSSLLSKIAKGF----GVESYTTLTGFKWLMNVGIAQSQPDNQF 394

Query: 428 LFAFEEAIGYMCCPFVLDKDGVSAAVICAELASFLATKNLSLSQQLNAIYVEYGYHITTA 487
           LFA+EEA+GY     V DKDG+SA V  A+L + LA K  ++  +L  IY E G+H+  A
Sbjct: 395 LFAYEEALGYTVGNMVWDKDGLSALVAFAQLTAELAAKGQTIWDRLEQIYREQGFHL-NA 453

Query: 488 SYFICHDQGTIQNLFGNLRNYDGKNNYPKMCGKFEISAIRDLTTGYDDSQPDKKAVLPTS 547
              I     T  N+   LR +      P   G+  + +  DL    +    D K      
Sbjct: 454 QVSIALKPDT-PNIGAYLREHP-----PLAIGEHALVSTDDL-KALERRFADGKVEKINL 506

Query: 548 KSSQMITFTFANGGVATMRTSGTEPKIKYYAELCAP 583
            +S ++T+  ANG    +R SGTEPKIK Y E+  P
Sbjct: 507 PASDVLTYRLANGARVIVRPSGTEPKIKCYYEVVEP 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: 874
Number of extensions: 43
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