Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_090272717.1 BLU11_RS07240 ABC transporter ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >NCBI__GCF_900105005.1:WP_090272717.1 Length = 357 Score = 150 bits (380), Expect = 3e-41 Identities = 87/230 (37%), Positives = 128/230 (55%), Gaps = 6/230 (2%) Query: 35 SRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDL 94 S G T+ + + SL I G+ ++G SGSGK+T + + PTSGE+ DG I + Sbjct: 14 SYDGDTLVVKNFSLDISKGEFLTMLGPSGSGKTTCLMMLAGFETPTSGEIRLDGQMINKM 73 Query: 95 GAKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLS 154 A R + MVFQ++AL PH T+ +N+ Y VR + K + + +D V + Sbjct: 74 ------APHKRGIGMVFQNYALFPHMTIAENLAYPLTVRKMPKAEIEQRVNTSLDMVEMR 127 Query: 155 GYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLA 214 + P QLSGG KQR+ LARAL + ++LMDE ALD +R MQ ++ +L L Sbjct: 128 DKKNRTPGQLSGGQKQRIALARALIFEPKLVLMDEPLGALDKNLREQMQYEIKRLHERLG 187 Query: 215 KTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264 T V++THD EAL + IA+ DG V QV +P+ + + PA +VA F+ Sbjct: 188 ITAVYVTHDQTEALTMSDRIAVFDDGIVQQVASPSVLYEEPATAFVANFI 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: 241 Number of extensions: 9 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: 357 Length adjustment: 27 Effective length of query: 248 Effective length of database: 330 Effective search space: 81840 Effective search space used: 81840 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 24 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