GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Desulfoscipio geothermicus DSM 3669

Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate WP_092483962.1 BM299_RS10985 FAD-linked oxidase C-terminal domain-containing protein

Query= SwissProt::Q7TNG8
         (484 letters)



>NCBI__GCF_900115975.1:WP_092483962.1
          Length = 458

 Score =  276 bits (707), Expect = 8e-79
 Identities = 162/461 (35%), Positives = 246/461 (53%), Gaps = 10/461 (2%)

Query: 27  LSQDFVEALKAVVGSPHVSTASAVREQHGHDESMHRCQPPDAVVWPQNVDQVSRVASLCY 86
           + +D V+ +K+VVGS +V  +   R  + +D +  R  P   VV P N  +V+ +  L  
Sbjct: 1   MDKDTVKKIKSVVGSEYVLESPEERICYSYDGTARRGIPA-LVVLPGNAREVAEIVRLAN 59

Query: 87  NQGVPIIPFGTGTGVEGGVCAVQGGVCINLTHMDQITELNTEDFSVVVEPGVTRKALNTH 146
            +G PI P G GTG+ GG    + G+ + L+ M++I E++ +D   VVEPGV    L+  
Sbjct: 60  EKGFPIFPRGAGTGLSGGSVPAEQGLAMVLSRMNRILEISRDDLLAVVEPGVVTGRLHRA 119

Query: 147 LRDSGLWFPVDPGA--DASLCGMAATGASGTNAVRYGTMRDNVINLEVVLPDGRLLHTAG 204
           +   GL++P DP +    ++ G  A  A G  A +YG  RD V+ LEVV P G +++T G
Sbjct: 120 VEKEGLFYPPDPSSLQTCTIGGNVAENAGGPRAFKYGVTRDYVLGLEVVTPTGEIINTGG 179

Query: 205 RGRHYRKSAAGYNLTGLFVGSEGTLGIITSTTLRLHPAPEATVAATCAFPSVQAAVDSTV 264
           R     K+  GY+LTGL  GSEGTLGIIT  TLRL P P A   A   +  V+ A  +  
Sbjct: 180 RTV---KNVTGYDLTGLLTGSEGTLGIITRITLRLVPKPRAVQTALAVYNRVEDAASTVT 236

Query: 265 QILQAAVPVARIEFLDDVMMDACNRHSKLNCPV--APTLFLEFHGSQQTLAEQLQRTEAI 322
            +++  +  A +E +D + +     + +L  P+     L +E  G    +AE+++  E  
Sbjct: 237 AMIRRGIIPATLELMDRITIRCVENYLRLGLPMDAGAILLIEVDGLPAQVAEEMKLVEDA 296

Query: 323 TQDNGGSHFSWAKEAEKRNELWAARHNAWYAALALSPGSKAYSTDVCVPISRLPEILVET 382
            + N       A +A +R  LW AR     A + + P     S D  VP S++PE++   
Sbjct: 297 CRQNSCRALQTATDAAERERLWKARRAVSTAIVQIKPTK--ISEDATVPRSKIPEMVERL 354

Query: 383 KEEIKASKLTGAIVGHVGDGNFHCILLVDPDDAEEQRRVKAFAENLGRRALALGGTCTGE 442
           K   +   L   + GH GDGN H  +LVD  D  E  + +   + + R AL LGGT +GE
Sbjct: 355 KSIGEKYGLHLPVFGHAGDGNLHPNILVDKRDPVEMEKAEKAVQEIFRAALDLGGTLSGE 414

Query: 443 HGIGLGKRQLLQEEVGPVGVETMRQLKNTLDPRGLMNPGKV 483
           HG+GL K+  L+ E G  G+E M+ +K  +DPR ++NPGK+
Sbjct: 415 HGVGLLKKPYLEWEAGAGGIEYMKAIKKAVDPRNVLNPGKI 455


Lambda     K      H
   0.318    0.133    0.403 

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: 543
Number of extensions: 22
Number of successful extensions: 5
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: 484
Length of database: 458
Length adjustment: 33
Effective length of query: 451
Effective length of database: 425
Effective search space:   191675
Effective search space used:   191675
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