GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Acidovorax sp. GW101-3H11

Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate Ac3H11_4909 D-Lactate dehydrogenase, cytochrome c-dependent (EC 1.1.2.4)

Query= SwissProt::F1QXM5
         (497 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4909
          Length = 474

 Score =  469 bits (1206), Expect = e-136
 Identities = 222/442 (50%), Positives = 313/442 (70%), Gaps = 3/442 (0%)

Query: 49  SVGSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGLEGG 108
           S+  AVREQHGRDE   +  PP  VVF  S ++V+   K+   Y +P+IP+G G+ LEG 
Sbjct: 36  SLAQAVREQHGRDEGSLQAPPPSAVVFAESTQDVADAVKLASQYEVPVIPYGAGSSLEGH 95

Query: 109 VGALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGADASL 168
           + A+QGG+   + +M QV+ ++ ED  VTV+PG+TRK+LN  ++DTGL+FP+DPGADAS+
Sbjct: 96  LLAVQGGISIDVSRMNQVLSINAEDLTVTVQPGITRKALNEAIKDTGLFFPIDPGADASI 155

Query: 169 CGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNLFVG 228
            GM AT ASGTNAVRYGTMRENVL LEVV A G ++HT   G R +K++AGY+LT L VG
Sbjct: 156 GGMCATRASGTNAVRYGTMRENVLALEVVTASGEVIHT---GTRAKKSSAGYDLTRLMVG 212

Query: 229 SEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDDVMI 288
           SEGTLGI+T+ T+RLY +PE++ +A+CSFPS+++AV +T+Q +Q GVPIAR+E +D   +
Sbjct: 213 SEGTLGIMTEITVRLYPLPEAVSAAICSFPSIEAAVRTTIQTIQIGVPIARVELIDHHTV 272

Query: 289 NACNRFNNLSYAVTPTLFLEFHGSSKSMEEQVSVTEEITRDNGGSDFAWAEDEETRSRLW 348
              N  + L+    P L +EFHGS  S++EQ  + ++I  + GG  F WA   E R+RLW
Sbjct: 273 RMVNAHSKLTLREEPMLLMEFHGSPASVKEQAEMVQDIASEFGGQAFEWASTPEERTRLW 332

Query: 349 KARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVETKADLISNNITGPIAGHVGDGNF 408
            ARH+A++AA+  RPGC+A STD CVPISRL   ++E+  ++ ++ I   + GHVGDGNF
Sbjct: 333 TARHNAYFAAVQSRPGCRAISTDTCVPISRLADCLLESVDEVEASGIPYFLVGHVGDGNF 392

Query: 409 HCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALLREEVGPLAIEV 468
           H   ++DPN  +E  +  +    L  RAL+M GTCTGEHG+G+ K   L +E G  A+++
Sbjct: 393 HFGYLIDPNSAEERTKAEAMNHTLVARALSMGGTCTGEHGVGVHKMGFLLDETGTGAVDM 452

Query: 469 MKGLKASLDPRNLMNPGKVLEL 490
           M+ +K +LDP+N++NPGK+  L
Sbjct: 453 MRAIKRALDPKNILNPGKIFAL 474


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: 553
Number of extensions: 20
Number of successful extensions: 2
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: 474
Length adjustment: 34
Effective length of query: 463
Effective length of database: 440
Effective search space:   203720
Effective search space used:   203720
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 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