GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Phaeobacter inhibens BS107

Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate GFF860 PGA1_c08740 glutamate dehydrogenase GluD

Query= BRENDA::P00366
         (558 letters)



>FitnessBrowser__Phaeo:GFF860
          Length = 476

 Score =  370 bits (951), Expect = e-107
 Identities = 214/498 (42%), Positives = 304/498 (61%), Gaps = 32/498 (6%)

Query: 63  DPNFFKMVEGFFDRGASIVEDKLVEDLKTRETEEQKRNRVRSILRIIKPCNHVLSLSFPI 122
           +P+F + V+  F+R  S+++  L   L+ +                I+ CN   ++ F +
Sbjct: 6   EPSFRQSVDLMFNRAVSLMD--LPPGLEEK----------------IRVCNATYTVRFGV 47

Query: 123 RRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGA 182
           R   G  +   GYR+ HS+H  P KGGIRY+  V+ DEV+ALA+LMTYKCA+V+ PFGG+
Sbjct: 48  RLRGGI-QTFTGYRSVHSEHMEPVKGGIRYAMGVNQDEVEALAALMTYKCALVEAPFGGS 106

Query: 183 KAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYAS 242
           K G+ I+P+ Y ++ELE ITRRF  ELAK+  I P  +VPAPDM TGEREM+WIAD YA 
Sbjct: 107 KGGLCIDPRQYEEHELELITRRFAYELAKRDLINPSQNVPAPDMGTGEREMAWIADQYA- 165

Query: 243 TIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDK 302
            +   DINA ACVTGKP++ GGI GR+ ATGRGV + +  F      ++   M      K
Sbjct: 166 RMNTTDINAKACVTGKPLNAGGIAGRVEATGRGVQYALREFFRNPEDVAAANMDGKLDGK 225

Query: 303 TFVVQGFGNVGLHSMRYL-HRFGAKCITVGESDGSIWNPDGIDPKELEDFKLQHGTILGF 361
             +VQG GNVG H+ ++L    GAK   V E DG + + +G+D + +  +   +G + G+
Sbjct: 226 RVIVQGLGNVGYHAAKFLMSEDGAKITAVIERDGGLIDENGLDIEAVFQWIANNGGVTGY 285

Query: 362 PKAKIYEGS--ILEVDCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLE 419
           P A+  E    +LE DCDILIPAA E  +  +NA  +KA++I E ANGP T  AD+I  +
Sbjct: 286 PDARYVENGALLLEEDCDILIPAALEGVINLTNAANIKARLIIEAANGPVTAGADEILRD 345

Query: 420 RNIMVIPDLYLNAGGVTVSYFEWLNNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFG 479
           +  ++IPD+Y NAGGVTVSYFEW+ NL+H+ +GR+  + E ++ + L++   E+L    G
Sbjct: 346 KGTVIIPDMYANAGGVTVSYFEWVKNLSHIRFGRMQRRQE-EARHQLVVDELEALSESLG 404

Query: 480 KHGGTIPIVPTAEFQDR-ISGASEKDIVHSGLAYTMERSARQIMRTAMK-YNLGLDLRTA 537
           K     P     +F +R + GA E ++V SGL  TM R+A Q MR      N   DLRTA
Sbjct: 405 KTWTLNP-----KFTERYLRGADELELVRSGLDDTM-RTAYQSMREVWHGRNDVTDLRTA 458

Query: 538 AYVNAIEKVFRVYNEAGV 555
           AY+ +I+KV + Y   G+
Sbjct: 459 AYLVSIDKVAKSYRAKGL 476


Lambda     K      H
   0.318    0.136    0.404 

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: 659
Number of extensions: 23
Number of successful extensions: 5
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: 558
Length of database: 476
Length adjustment: 35
Effective length of query: 523
Effective length of database: 441
Effective search space:   230643
Effective search space used:   230643
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 (21.7 bits)
S2: 52 (24.6 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