GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Dethiosulfovibrio salsuginis USBA 82

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_085544045.1 B9Y55_RS03840 hydroxyacid dehydrogenase

Query= BRENDA::Q9I530
         (329 letters)



>NCBI__GCF_900177735.1:WP_085544045.1
          Length = 316

 Score =  162 bits (409), Expect = 1e-44
 Identities = 103/306 (33%), Positives = 159/306 (51%), Gaps = 17/306 (5%)

Query: 23  HGFELHFQQAHLQADTAVLAQGFEVVCAFVNDDLSRPVLERLAAGGTRLVALRSAGYNHV 82
           H FE + +   ++ +   LA     + A  N  L   V+   +    +++++   GY+HV
Sbjct: 28  HSFEAYCRSDDVKENVKRLAGADVAIIA--NMPLGGQVIS--SCDRLKMISVAFTGYDHV 83

Query: 83  DLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTREGDFSLHGLTGFDL 142
           D+ +  +  + V +   YS  +V E A+GL L + R++       R G  +  GL G  L
Sbjct: 84  DMESCLSKRITVSNCAGYSTDSVVELALGLSLAVVRKIVPCDGAVRAGK-TKDGLIGNQL 142

Query: 143 HGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNPRIQALGGRYLALDALLAESDIVS 202
            GK VG++GTG IG   A +    GC ++AY       + ++G  YL+L  L++  D++S
Sbjct: 143 AGKTVGIVGTGAIGVKVAAVFKALGCNVVAYSRSQRDEVLSMGIPYLSLKDLMSSCDLIS 202

Query: 203 LHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALIEALKSGQLGYLGLDVYEE 262
           LH P   +T  LID   +++MK  + LINT RG +V+  AL +ALKSG +   G+DV++ 
Sbjct: 203 LHLPCNGETAGLIDRDMISSMKRSSFLINTARGPIVDNKALADALKSGSIAGAGIDVFDM 262

Query: 263 EADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREALAAIADTTLDNIAAWQDGT 322
           E           PL +     LL  PN V+T H AF T EAL + A   +DN+  W DG 
Sbjct: 263 E----------PPLLEGY--PLLDAPNCVLTPHVAFATPEALQSRAVIAIDNVRLWMDGK 310

Query: 323 PRNRVR 328
           P+N VR
Sbjct: 311 PQNVVR 316


Lambda     K      H
   0.323    0.137    0.402 

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: 239
Number of extensions: 12
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: 329
Length of database: 316
Length adjustment: 28
Effective length of query: 301
Effective length of database: 288
Effective search space:    86688
Effective search space used:    86688
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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