Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 14345 b0199 DL-methionine transporter subunit (NCBI)
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Keio:14345 Length = 343 Score = 159 bits (403), Expect = 6e-44 Identities = 86/223 (38%), Positives = 130/223 (58%), Gaps = 1/223 (0%) Query: 43 LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102 LN+VSL + AG+I+ ++G SG+GKSTL+R +N L PT G VL DG + L L Sbjct: 21 LNNVSLHVPAGQIYGVIGASGAGKSTLIRCVNLLERPTEGSVLVDGQELTTLSESELTKA 80 Query: 103 RMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPH 162 R R++ M+FQ F L+ RTV NV + KD+ + + + VGL +P Sbjct: 81 R-RQIGMIFQHFNLLSSRTVFGNVALPLELDNTPKDEVKRRVTELLSLVGLGDKHDSYPS 139 Query: 163 QLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITH 222 LSGG KQRV +ARALA++ V+L DEA SALDP + + L + R L TI+ ITH Sbjct: 140 NLSGGQKQRVAIARALASNPKVLLCDEATSALDPATTRSILELLKDINRRLGLTILLITH 199 Query: 223 DLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFVQ 265 ++D RI +A++ +G++++ T +++ +P +F+Q Sbjct: 200 EMDVVKRICDCVAVISNGELIEQDTVSEVFSHPKTPLAQKFIQ 242 Lambda K H 0.323 0.139 0.397 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: 197 Number of extensions: 6 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: 275 Length of database: 343 Length adjustment: 27 Effective length of query: 248 Effective length of database: 316 Effective search space: 78368 Effective search space used: 78368 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 (21.9 bits) S2: 48 (23.1 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