Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 152 bits (385), Expect = 8e-42 Identities = 89/226 (39%), Positives = 133/226 (58%), Gaps = 10/226 (4%) Query: 43 LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102 ++ VS ++ AG+I ++G SG GK+TL+R I SG + G+ + A A R+ Sbjct: 24 VDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETV----ATAQRSL 79 Query: 103 --RMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKF 160 R V MVFQ +AL PH TVL NV +G R R S AR+ + VGL G + ++ Sbjct: 80 PPETRSVGMVFQDYALFPHLTVLDNVCFGLRDRKGSAAVARQA----LALVGLEGLERRY 135 Query: 161 PHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFI 220 PH+LSGG +QRV LARALA +IL+DE S LD +R ++ +L + R T + + Sbjct: 136 PHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQAQATAILV 195 Query: 221 THDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFVQR 266 THD +EAL I +A++R G+ Q+G P ++ +PA+ +VA F+ + Sbjct: 196 THDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLSQ 241 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: 238 Number of extensions: 8 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: 368 Length adjustment: 27 Effective length of query: 248 Effective length of database: 341 Effective search space: 84568 Effective search space used: 84568 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