Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_086509734.1 BZY95_RS09705 ABC transporter ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >NCBI__GCF_002151265.1:WP_086509734.1 Length = 313 Score = 184 bits (467), Expect = 2e-51 Identities = 99/231 (42%), Positives = 142/231 (61%), Gaps = 6/231 (2%) Query: 32 DILSRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNI 91 D+ R G ++ +SL++ G++ ++G SG GKST +R INRLIE GE+ DG + Sbjct: 6 DVTKRFGDETAVDGISLRVEKGELCALVGTSGCGKSTTLRMINRLIEHDGGEIHLDGQPV 65 Query: 92 LDLGAKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTV 151 ALR RR+ V QS L PH TV +N+ R+ K R+ + + + Sbjct: 66 RSFDEVALR----RRIGYVIQSTGLFPHWTVARNIGLVPRLLKWPKGKVRDRVEELMQLL 121 Query: 152 GL--SGYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQL 209 GL + + K+P QLSGG QRVG+ARALAAD D++LMDE F ALDP+ R +QD+L L Sbjct: 122 GLPVAEFADKYPRQLSGGQAQRVGVARALAADPDILLMDEPFGALDPITRATLQDELRVL 181 Query: 210 QRNLAKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYV 260 Q L KT+VF+THD+DEAL + + ++ G++VQ G+P ++L PAN +V Sbjct: 182 QARLHKTVVFVTHDMDEALALADRLVVMHQGRIVQQGSPVELLREPANPFV 232 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: 236 Number of extensions: 13 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: 313 Length adjustment: 26 Effective length of query: 249 Effective length of database: 287 Effective search space: 71463 Effective search space used: 71463 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