GapMind for catabolism of small carbon sources

 

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

Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate 5209194 Shew_1672 3-hydroxyisobutyrate dehydrogenase (RefSeq)

Query= BRENDA::Q8ZLV8
         (296 letters)



>FitnessBrowser__PV4:5209194
          Length = 299

 Score =  168 bits (425), Expect = 2e-46
 Identities = 98/294 (33%), Positives = 162/294 (55%), Gaps = 10/294 (3%)

Query: 5   VGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVIIT 64
           V FIGLG MG PM+ NL+KAGY++   D +  A++ V+  GA  A +A A A   DV+IT
Sbjct: 4   VAFIGLGNMGGPMAVNLVKAGYTVKAFDLSQTALSHVVEEGAMQAPSACAAAAAADVVIT 63

Query: 65  MLPNSPHVKEVALGEN---GIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAP 121
           MLP   HV+ + LG+    GII+    GT+LID S+I   ++R +++  K KG+E +DAP
Sbjct: 64  MLPAGKHVRSLYLGDEQNKGIIDVVADGTLLIDCSTIDAESARFVAEQAKTKGLEFIDAP 123

Query: 122 VSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVAL 181
           VSGG   A  GTL+ + GG    F++   ++  M  ++ H G  GAG V K+ N +++++
Sbjct: 124 VSGGTAGAAAGTLTFICGGSDTAFEQAQGVLNVMGANIFHAGGPGAGQVAKICNNMLLSV 183

Query: 182 NIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDA--KAPMVMD-----RNFKPGFR 234
            +   SE++ +    G++P ++ + ++    G+  LD     P VM+       ++ GF 
Sbjct: 184 LMVGTSESIQMGIDHGLDPKVLSEIMKVSSGGNWTLDKYNPCPDVMENVPSSNGYQGGFM 243

Query: 235 IDLHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSALACYYEK 288
           +DL +KDL  + + +    +  P+ A    +       G+G  D S++   + K
Sbjct: 244 VDLMVKDLGLSQEAALLSNSSTPMGALARSLYVNHARQGNGKRDFSSIFEQFNK 297


Lambda     K      H
   0.316    0.132    0.367 

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: 219
Number of extensions: 10
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: 296
Length of database: 299
Length adjustment: 26
Effective length of query: 270
Effective length of database: 273
Effective search space:    73710
Effective search space used:    73710
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: 48 (23.1 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