GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Sinorhizobium meliloti 1021

Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate SM_b21129 SM_b21129 oxidoreductase

Query= SwissProt::F1QXM5
         (497 letters)



>FitnessBrowser__Smeli:SM_b21129
          Length = 442

 Score =  181 bits (459), Expect = 5e-50
 Identities = 139/451 (30%), Positives = 209/451 (46%), Gaps = 28/451 (6%)

Query: 51  GSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGLEGGVG 110
           G  + E+H  D S+     P  VV P SV EV+   +IC+ +R  ++P G  TGL GG  
Sbjct: 4   GDRIAERHRGDASLTGRILPLAVVRPASVAEVADALRICNAHRQAVVPQGGLTGLAGGAN 63

Query: 111 ALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGADAS--L 168
              G V  SL ++  + ++      +TV  G   +       D G   P+D GA  S  +
Sbjct: 64  PCAGDVAISLERLSGIEEIDAAAGTMTVLAGTPLEVAQRAAEDAGFLLPIDLGARGSCQV 123

Query: 169 CGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNLFVG 228
            G  AT+A G   +R G  R+NVL LE VLADGT+L +  K     K   GY+L  LF+G
Sbjct: 124 GGNLATNAGGIRVIRNGVARDNVLGLEAVLADGTVLSSMNK---MIKNNTGYDLRQLFIG 180

Query: 229 SEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDDVMI 288
           SEGTLGIIT+A LRL  +P   ++A+C+  S ++ V     + +A   +A +    + M 
Sbjct: 181 SEGTLGIITRAVLRLRPLPAGRLTALCALDSYENVV---ALLKRAQKELAGLSAY-EAMW 236

Query: 289 NACNRFNNLS-----YAVTPTLFL----EFHGSSKSMEEQVSVTEEITRDNGGSDFAWAE 339
            +  RFN ++     +  TP   +    +  G     E   +       D    D   A+
Sbjct: 237 ESYFRFNCVAEGLRLFEATPAFAVIVEEDLQGHEAERERFEAFLGRALEDGVIGDALIAQ 296

Query: 340 DEETRSRLWKARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVETKADLISNNITGPI 399
            ++     W+ R       + L       + DV +PI  + +   E    L +      +
Sbjct: 297 SQKEVQTFWRIREGHALDRLPL-----LLNFDVSLPIGEIGRFADECGKALRAKFPEAHV 351

Query: 400 A--GHVGDGNFHCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALL 457
           +  GHVGD N H    + P  T+E    H+    +        G+ + EHGIGL KR  L
Sbjct: 352 SFFGHVGDSNLHIAFSV-PGATEET--AHAVDAVVYGLVGIYSGSVSAEHGIGLVKRDFL 408

Query: 458 REEVGPLAIEVMKGLKASLDPRNLMNPGKVL 488
                P  +E+M+ +K +LDP  ++NPGKVL
Sbjct: 409 DRSRSPAELELMRRIKNALDPNGILNPGKVL 439


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: 446
Number of extensions: 16
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: 497
Length of database: 442
Length adjustment: 33
Effective length of query: 464
Effective length of database: 409
Effective search space:   189776
Effective search space used:   189776
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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