Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 16237 b2129 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Keio:16237 Length = 308 Score = 182 bits (463), Expect = 6e-51 Identities = 100/230 (43%), Positives = 143/230 (62%), Gaps = 5/230 (2%) Query: 38 GCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAK 97 G +ND++L G V++G SGSGKST ++ INRL+E SGE+ F G+ I L Sbjct: 12 GAQKAVNDLNLNFQEGSFSVLIGTSGSGKSTTLKMINRLVEHDSGEIRFAGEEIRSLPVL 71 Query: 98 ALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGL-SGY 156 LR RR+ QS L PH +V QN+ +++ S+ + + + +GL S Sbjct: 72 ELR----RRMGYAIQSIGLFPHWSVAQNIATVPQLQKWSRARIDDRIDELMALLGLESNL 127 Query: 157 DAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKT 216 ++PHQLSGG +QRVG+ARALAAD V+LMDE F ALDP+ RG +Q ++ ++ R L +T Sbjct: 128 RERYPHQLSGGQQQRVGVARALAADPQVLLMDEPFGALDPVTRGALQQEMTRIHRLLGRT 187 Query: 217 IVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFVQR 266 IV +THD+DEALR+ + ++ G+VVQ G P +L PAND+V +F R Sbjct: 188 IVLVTHDIDEALRLAEHLVLMDHGEVVQQGNPLTMLTRPANDFVRQFFGR 237 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: 235 Number of extensions: 9 Number of successful extensions: 3 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: 308 Length adjustment: 26 Effective length of query: 249 Effective length of database: 282 Effective search space: 70218 Effective search space used: 70218 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