GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Shewanella loihica PV-4

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate 5208375 Shew_0887 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (RefSeq)

Query= curated2:Q9YAW4
         (335 letters)



>FitnessBrowser__PV4:5208375
          Length = 317

 Score =  177 bits (449), Expect = 3e-49
 Identities = 109/285 (38%), Positives = 161/285 (56%), Gaps = 5/285 (1%)

Query: 40  LLSKAREADALYTLLTDRIDCDLLSQAPRLRIVAQMAVGFDNIDVECATRLGIYVTNTPG 99
           LL +A+ A  L T  T  +D D L   P L  +  +A G + +D+  A  LGI VTN PG
Sbjct: 38  LLDRAQGAQVLLTNKTV-LDADALRALPDLEYIGVLATGTNVVDLNAARELGIKVTNVPG 96

Query: 100 VLTEATAEFTWALILAAARRVVEADHFVRWGEWWRLRTGWHPMMMLGVELRGKTLGILGM 159
              +A A+  +A IL   +R+ +  + V  G W +       +  L   L+GKTLG++G 
Sbjct: 97  YGPDAVAQMVFAHILHHTQRLSDHHNAVVAGAWSQAPDFCFTLAPLQ-SLKGKTLGLVGF 155

Query: 160 GRIGSRVAEIGKAFGMRIIYHSRSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTDET 219
           G IG +VA I KAF MR++ ++ S K ++ +  G  +   E L   +DI+S+H PLT +T
Sbjct: 156 GDIGRQVANIAKAFQMRVLVNTPSIKHDLPE--GVSWCEREALFASADIISLHCPLTPDT 213

Query: 220 RHLIGESELKLMKKTAILVNTGRGAIVDTGALVKALREGWIAAAALDVFEEEPLNPNHPL 279
             LI    L  MK  AIL+NT RG +VD  AL  AL +G IAAA +DV   EP   ++PL
Sbjct: 214 EKLINRERLSAMKPNAILINTARGGLVDEQALANALAQGEIAAAGVDVLSSEPPQADNPL 273

Query: 280 TAFKNVVLAPHAASATRETRLRMAMMAAENLVAFAQGKVPPNLVN 324
            +  ++ ++PH + AT+E R ++  +A +NL  +  G+ P NLVN
Sbjct: 274 LSAPHISISPHNSWATKEARQQLLTIAVDNLKGYLAGQ-PMNLVN 317


Lambda     K      H
   0.322    0.136    0.406 

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: 260
Number of extensions: 13
Number of successful extensions: 3
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: 335
Length of database: 317
Length adjustment: 28
Effective length of query: 307
Effective length of database: 289
Effective search space:    88723
Effective search space used:    88723
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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