Align Lactate utilization protein C (characterized)
to candidate 14446 b0308 putative transporter (VIMSS)
Query= SwissProt::Q81GA3 (236 letters) >FitnessBrowser__Keio:14446 Length = 231 Score = 147 bits (370), Expect = 2e-40 Identities = 80/233 (34%), Positives = 133/233 (57%), Gaps = 6/233 (2%) Query: 5 IQNRDAFLDNIAKELGRARKTEGVERPVWKSNVNIETLKDYSQEELLEVFKKQCTNIHTT 64 + NR FL+N+A+ LGR + E +N E L +Q++ + F + +++ T Sbjct: 1 MDNRGEFLNNVAQALGRPLRLEPQAEDAPLNNYANERLTQLNQQQRCDAFIQFASDVMLT 60 Query: 65 VVETTND-RLGEDLQKVIMENGGGPILLSADDRFDAYGLTSLFKEELPKRDVEVNVWDPE 123 E T++ + E ++ E G +++S D R + G++ ++E VWDP Sbjct: 61 RCELTSEAKAAEAAIRLCKELGDQSVVISGDTRLEELGISERLQQEC-----NAVVWDPA 115 Query: 124 RKDENMRLAEKANIGIAFSDYTLAESGTIVVQSHKGQGRSLHFLPTVYFAIIPRETLVPR 183 + EN+ AE+A +G+ +++Y L ESG +V+ S +GRSL LP I+ + T++PR Sbjct: 116 KGAENISQAEQAKVGVVYAEYGLTESGGVVLFSAAERGRSLSLLPEYSLFILRKSTILPR 175 Query: 184 ITQAVQDMNSHVENGETAASCINFITGPSNSADIEMNLVVGVHGPLKAVYFIV 236 + Q + ++ + GE SCIN I+GPS++ADIE+ VVGVHGP+KAVY I+ Sbjct: 176 VAQLAEKLHQKAQAGERMPSCINIISGPSSTADIELIKVVGVHGPVKAVYLII 228 Lambda K H 0.316 0.134 0.383 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: 142 Number of extensions: 4 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: 236 Length of database: 231 Length adjustment: 23 Effective length of query: 213 Effective length of database: 208 Effective search space: 44304 Effective search space used: 44304 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 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