GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutA in Desulfovibrio vulgaris Hildenborough

Align Lactate utilization protein A (characterized)
to candidate 208547 DVU3033 iron-sulfur cluster-binding protein

Query= SwissProt::Q81GA5
         (239 letters)



>MicrobesOnline__882:208547
          Length = 717

 Score =  143 bits (361), Expect = 8e-39
 Identities = 89/242 (36%), Positives = 132/242 (54%), Gaps = 10/242 (4%)

Query: 1   MKVTLFVTCLVDMFETNVGKATVEVLERLGCEIEFPEAQVCCGQPAYNSGHVEAAKEAMK 60
           +++ LF  C+ D       KA V+V+     +I+FP  Q CCG P    G  EA  E  +
Sbjct: 474 LRIALFSGCVQDFVYPEQMKAAVKVIASQNVDIDFPMDQSCCGLPVQMMGEREATIEVAR 533

Query: 61  HMIETFEDA--EYIVTPSGSCATMFHE-YPHVFKDDPKWAKRAQKVADKTYEFTQFIVDV 117
             +  F+ A  +YIVT   SCA+   E YP +    P+   R ++ ++K  +F+ F+ DV
Sbjct: 534 QNVMAFDAARYDYIVTLCASCASHLKETYPKLLTGHPEMTTRVRQFSNKIIDFSSFVHDV 593

Query: 118 LKVTD---VGASLPGIATIHKSCHMTRMLGVKEAPGILLSNVKGLTVRDLPNVQNCCGFG 174
           L +      G S   +A  H SCH+ R LGV E P  L++   G T         CCGFG
Sbjct: 594 LGMKSDAFKGGSNEKVA-YHSSCHLCRGLGVVEQPRNLIA-ASGATYCKAEEEDVCCGFG 651

Query: 175 GTFSVKMTPISEQMVDEKVDSVMETGADYLIGADC-GCLLNIGGRIERLGKEVKVMHIAE 233
           GTFS K   +S +++ +K+D+V  TGA  L+ ADC GC++ + G +E+ G +VKV H+AE
Sbjct: 652 GTFSAKFPELSAELLRKKLDNVEATGAGRLV-ADCPGCIMQLRGGMEKRGGKVKVGHVAE 710

Query: 234 VL 235
           +L
Sbjct: 711 LL 712


Lambda     K      H
   0.320    0.135    0.407 

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: 438
Number of extensions: 31
Number of successful extensions: 4
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: 239
Length of database: 717
Length adjustment: 31
Effective length of query: 208
Effective length of database: 686
Effective search space:   142688
Effective search space used:   142688
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: 50 (23.9 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