GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctD in Desulfoscipio geothermicus DSM 3669

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate WP_092483962.1 BM299_RS10985 FAD-linked oxidase C-terminal domain-containing protein

Query= BRENDA::H6LBS1
         (466 letters)



>NCBI__GCF_900115975.1:WP_092483962.1
          Length = 458

 Score =  295 bits (756), Expect = 2e-84
 Identities = 172/463 (37%), Positives = 258/463 (55%), Gaps = 7/463 (1%)

Query: 6   VEASDIAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAY 65
           ++   +  IK ++ +E V    E    +S+D        P +++   +  EV++I++ A 
Sbjct: 1   MDKDTVKKIKSVVGSEYVLESPEERICYSYDGTAR-RGIPALVVLPGNAREVAEIVRLAN 59

Query: 66  EHNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKF 125
           E   P+  RG+GTGL G  VP   G+ +  + MN ILE+  ++L   VEPGV+   L + 
Sbjct: 60  EKGFPIFPRGAGTGLSGGSVPAEQGLAMVLSRMNRILEISRDDLLAVVEPGVVTGRLHRA 119

Query: 126 VEENDLFYPPDPGE-KSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGG 184
           VE+  LFYPPDP   ++ TI GN++ NAGG RA KYGVTRDYV GL VV   GEII  GG
Sbjct: 120 VEKEGLFYPPDPSSLQTCTIGGNVAENAGGPRAFKYGVTRDYVLGLEVVTPTGEIINTGG 179

Query: 185 KIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKII 244
           + VKN +GY L  L+ GSEGTL +IT+  L+L+P P+   + L  +  + DAA  V  +I
Sbjct: 180 RTVKNVTGYDLTGLLTGSEGTLGIITRITLRLVPKPRAVQTALAVYNRVEDAASTVTAMI 239

Query: 245 KSKAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLC 304
           +   IP  +E M+R TI   E++L    P   + A +L+  DG    QV  E + V + C
Sbjct: 240 RRGIIPATLELMDRITIRCVENYLRLGLP-MDAGAILLIEVDG-LPAQVAEEMKLVEDAC 297

Query: 305 LAEGAKDVYIVDTVERKDSVWSARGAFLEAI-KASTTEMDECDVVVPRNRIAEFIEFTHD 363
                + +        ++ +W AR A   AI +   T++ E D  VPR++I E +E    
Sbjct: 298 RQNSCRALQTATDAAERERLWKARRAVSTAIVQIKPTKISE-DATVPRSKIPEMVERLKS 356

Query: 364 LAKEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVSGEH 423
           + ++  + +P FGHAGDGNLH  +  D+    + E K  +A+  ++  AL   G +SGEH
Sbjct: 357 IGEKYGLHLPVFGHAGDGNLHPNILVDKRDPVEME-KAEKAVQEIFRAALDLGGTLSGEH 415

Query: 424 GIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKVCQM 466
           G+G  K+ YL  + G   +  M  IK+  DP+N+LNP K+ Q+
Sbjct: 416 GVGLLKKPYLEWEAGAGGIEYMKAIKKAVDPRNVLNPGKIFQV 458


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: 496
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: 458
Length adjustment: 33
Effective length of query: 433
Effective length of database: 425
Effective search space:   184025
Effective search space used:   184025
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 Apr 09 2024. 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