GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Skermanella stibiiresistens SB22

Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate WP_037458870.1 N825_RS27050 FAD-binding protein

Query= BRENDA::O29853
         (443 letters)



>NCBI__GCF_000576635.1:WP_037458870.1
          Length = 495

 Score =  228 bits (581), Expect = 3e-64
 Identities = 156/448 (34%), Positives = 238/448 (53%), Gaps = 23/448 (5%)

Query: 13  VFPPSDAYRFDETPPLVAPRAAENFVVVKPSNSEEVSAILKFANEKSIPVFMRGGGTGLS 72
           V    D  R  ET  L A R     VVV P+ +E+VS +LK+ NE  I V  RG GT LS
Sbjct: 30  VIAERDEMRVYETDALTAYRQLP-MVVVLPNTTEQVSQVLKYCNEVGIKVVPRGAGTSLS 88

Query: 73  GGAVPTEEGIVLSTEKMTEL-EVDADNRVAICGAGVTLKQLDDAAFRHGLSFPPHPGAET 131
           GGA+P  +GI+L   K  ++ ++D  NR      GVT   + +A    G  + P P ++ 
Sbjct: 89  GGALPLADGIILGLGKFNKIVDIDYANRTVTAQPGVTNLGITNAVAHEGFYYAPDPSSQI 148

Query: 132 A-TVGGMIATNAGGVRALKYGTMRNYVLSLEAVLADGRIINVGGKTIKNSSGYSLLHLLV 190
           A T+GG IA N+GGV  LKYG   N VL +E VL +G II +GGK + +S GY LL ++ 
Sbjct: 149 ACTIGGNIAENSGGVHCLKYGLTTNNVLGIEMVLMNGDIIRLGGKHL-DSDGYDLLGVMT 207

Query: 191 GSEGTLAVITKATIRLFPQMRDMTVLAIPFPTMEDAMNCVVE-VARKMLPMALEFMEKRA 249
           GSEG L V+T+ T+R+  +   +  L I FP+ E   +CV   +A  ++P  +E M+K A
Sbjct: 208 GSEGLLGVVTEVTVRILRKPETLRALLIGFPSSESGGDCVAAIIAAGIIPGGMEMMDKPA 267

Query: 250 VEIGEKVSGERWVSREGEAHLLMVFESFDEAE------EAAKIAQSLGAIDVYAATTKKD 303
           +   E+     +   + EA LL+V     EAE      E  KIA + GA+ +  + ++ +
Sbjct: 268 IHAAEEFVHAGY-PMDVEA-LLIVELDGPEAEVHHLIGEVEKIALTCGAVSIRISESEDE 325

Query: 304 QDRLLKVRGMIYEGLRKEVIEVL--DACVPPAKIAEYWRRSNELAEEYGIELITYGHAGD 361
           +      R   +  + +   + L  D  +P  ++     R  E++ ++G+ +    HAGD
Sbjct: 326 RMVFWAGRKAAFPAVGRISPDYLCMDGTIPRKQLPLVLTRMAEMSVKHGLRVANVFHAGD 385

Query: 362 GNVHQHPLVY-----EGWEKSYFEFRKSLLSLAVSLGGVISGEHGIGAVKLSELEELFPE 416
           GN+  HPL+       G  ++  +F   +L L V +GGV++GEHG+G  K   +   F E
Sbjct: 386 GNL--HPLILYDANKPGELQAAEDFGADILKLCVEVGGVLTGEHGVGVEKRDLMNHQFTE 443

Query: 417 -QFELMRQIKLLFDPKNILNPGKVVRKL 443
                 +++K  FDP+ +LNPGKV  +L
Sbjct: 444 VDLNQQQRVKCAFDPEALLNPGKVFPQL 471


Lambda     K      H
   0.317    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: 518
Number of extensions: 29
Number of successful extensions: 6
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: 443
Length of database: 495
Length adjustment: 33
Effective length of query: 410
Effective length of database: 462
Effective search space:   189420
Effective search space used:   189420
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