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.
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:
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