GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctD in Thermoactinomyces daqus H-18

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate WP_033102282.1 JG50_RS0116910 FAD-binding protein

Query= BRENDA::H6LBS1
         (466 letters)



>NCBI__GCF_000763315.1:WP_033102282.1
          Length = 470

 Score =  292 bits (748), Expect = 1e-83
 Identities = 173/460 (37%), Positives = 261/460 (56%), Gaps = 12/460 (2%)

Query: 10  DIAAIKELI---PAERVFVGTEIGEDFSHDELGSIHSY-PEVLIKVTSTEEVSKIMKYAY 65
           D + +KELI     ERV +  +    ++ D   S  +Y P+V++   S  E+++IMK A 
Sbjct: 4   DPSIVKELIRITDEERVLLSLDERYTYAFD--ASFGTYLPDVVVFPQSATEIAEIMKLAN 61

Query: 66  EHNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKF 125
              IPV  RG GT L G  +P+ GGI+L  T MN +L +D +NL   VEPG+   EL + 
Sbjct: 62  REQIPVTPRGGGTSLSGGPLPVAGGIVLAMTRMNKLLRIDRDNLIAFVEPGITTAELQRE 121

Query: 126 VEENDLFYPPDPGEKS-ATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGG 184
            E+  LFYPPDP   + +TI GN++ N+GG   +KYGVT+ YV GL VV   GEII  GG
Sbjct: 122 AEKAGLFYPPDPSSSNVSTIGGNLAENSGGPHGLKYGVTKHYVIGLEVVTPQGEIIRTGG 181

Query: 185 KIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKII 244
             VKN +GY L  L++GSEGTL +ITKA+L+L+P P    +L+  F+ I D+   +  I+
Sbjct: 182 MTVKNVTGYDLTSLIVGSEGTLGIITKAVLRLIPKPPARKALMAIFDEIVDSGRAISGIL 241

Query: 245 KSKAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLC 304
           K+  +P  +E M++ +I   E++     P  ++ A +LL  DG+    V+ E    A +C
Sbjct: 242 KNGILPAKLEMMDQASIRAVENYQPSGLPLDAA-AILLLEVDGH-PAAVDEEIRKAAQIC 299

Query: 305 LAEGAKDVYIVDTVERKDSVWSARGAFLEAI-KASTTEMDECDVVVPRNRIAEFIEFTHD 363
               A++V +      +  +W AR     AI +   T++ E D  VPR++I E +E    
Sbjct: 300 RQYAAREVRLAADEAERAELWKARKLVSPAISQVKPTKISE-DATVPRSKIPEMLERLRQ 358

Query: 364 LAKEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVSGEH 423
           + ++  + +  FGHAGDGNLH  +  D     D   ++ EA+  ++  A+   G +SGEH
Sbjct: 359 IREKYQLHLVVFGHAGDGNLHPNIIADSR-DRDEMKRVEEAVAEIFKAAVELGGTLSGEH 417

Query: 424 GIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463
           GIG  K  ++  + G+  L +M  IKQ +DP N+LNP K+
Sbjct: 418 GIGTMKPAFMEMELGSAGLDMMRRIKQAWDPNNILNPFKI 457


Lambda     K      H
   0.318    0.136    0.388 

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: 502
Number of extensions: 24
Number of successful extensions: 4
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: 466
Length of database: 470
Length adjustment: 33
Effective length of query: 433
Effective length of database: 437
Effective search space:   189221
Effective search space used:   189221
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: 51 (24.3 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