GapMind for catabolism of small carbon sources

 

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

Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate WP_037457682.1 N825_RS23825 FAD-binding protein

Query= SwissProt::F1QXM5
         (497 letters)



>NCBI__GCF_000576635.1:WP_037457682.1
          Length = 466

 Score =  535 bits (1378), Expect = e-156
 Identities = 262/464 (56%), Positives = 338/464 (72%), Gaps = 5/464 (1%)

Query: 27  AKTAAVERVVSSFRSVTGDEGVSVGSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALA 86
           A+  A E ++   R + GD  +S  +AVRE HG+DES H   PPD V F +S EEV+A+ 
Sbjct: 8   ARAPAAEALIEELRGLLGDR-LSTSAAVREHHGKDESYHPVVPPDAVAFVQSTEEVAAVV 66

Query: 87  KICHHYRLPIIPFGTGTGLEGGVGALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKS 146
             C  +  P+IPFGTGT LEGGV AL GGVC  L  M  V+ +  ED DVTV+ GVTRK 
Sbjct: 67  AACARHDTPVIPFGTGTSLEGGVAALHGGVCIDLSGMNAVLRVSPEDLDVTVQAGVTRKQ 126

Query: 147 LNSYLRDTGLWFPVDPGADASLCGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHT 206
           LN +LRDTGL+FP+DPGADASL GMA+T ASGTNAVRYGTMRENVL L VV+ADG I+ T
Sbjct: 127 LNEHLRDTGLFFPIDPGADASLGGMASTRASGTNAVRYGTMRENVLGLTVVMADGRIVKT 186

Query: 207 AGKGRRPRKTAAGYNLTNLFVGSEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDS 266
            G   R RK+AAGY+LT LFVG+EGTLG+IT+ TLRLYG+PE++ +AVC FP+++ AVD+
Sbjct: 187 GG---RARKSAAGYDLTRLFVGAEGTLGVITEVTLRLYGIPEAISAAVCPFPTIKDAVDT 243

Query: 267 TVQILQAGVPIARIEFLDDVMINACNRFNNLSYAVTPTLFLEFHGSSKSMEEQVSVTEEI 326
            +  +Q+G+P+ARIE LD+V + A    + L YAV PTLF EFHG+   + EQ  +   I
Sbjct: 244 VITTIQSGIPVARIELLDEVQMRAVVAHSKLDYAVAPTLFFEFHGTEAGVTEQAEMVSAI 303

Query: 327 TRDNGGSDFAWAEDEETRSRLWKARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVET 386
             + GG+DF WA   E RSRLW+ARH+A+YAA+ALRPG K ++TDVCVPISRL + IVET
Sbjct: 304 AAEFGGTDFQWAAKAEDRSRLWQARHEAYYAALALRPGSKGWATDVCVPISRLAECIVET 363

Query: 387 KADLISNNITGPIAGHVGDGNFHCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGE 446
           KAD+ ++++T P+ GHVGDGNFH + ++DP +  E++      ER+  RALAM GTCTGE
Sbjct: 364 KADIAASSLTAPLVGHVGDGNFHLVYLVDPANPAELEEAAELNERMVMRALAMGGTCTGE 423

Query: 447 HGIGLGKRALLREEVGPLAIEVMKGLKASLDPRNLMNPGKVLEL 490
           HG+G GK   L  E G  A+ VM+ +K +LDP+N+MNPGKV+ +
Sbjct: 424 HGVGYGKMHFLPAEHGE-AVSVMRMVKQALDPKNIMNPGKVIRV 466


Lambda     K      H
   0.319    0.135    0.399 

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: 591
Number of extensions: 21
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: 497
Length of database: 466
Length adjustment: 34
Effective length of query: 463
Effective length of database: 432
Effective search space:   200016
Effective search space used:   200016
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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