Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >NCBI__GCF_000230695.2:WP_015448118.1 Length = 255 Score = 149 bits (375), Expect = 8e-41 Identities = 92/238 (38%), Positives = 129/238 (54%), Gaps = 5/238 (2%) Query: 36 RSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLG 95 R G L VSL AG ++G SGSGKST++R + L P G V DG + Sbjct: 20 RYGRLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGRPLQRSD 79 Query: 96 AKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGL-S 154 LR RRV V Q L PH T L N+ R G +++ R+ + L + Sbjct: 80 VLPLR----RRVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIRQRAEQLAALTHLPT 135 Query: 155 GYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLA 214 G ++P +LSGG +QRV L RAL AD D +L+DE ALDP++R ++QD+L Q+ L Sbjct: 136 GVLERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDPVVRHELQDELKQIFDQLG 195 Query: 215 KTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFVQRRHERPQ 272 KT++ +THDL EA + +LR G V+Q GT D+ + PA+ +V RFV + P+ Sbjct: 196 KTVIVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNRFVAAQRRLPE 253 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: 194 Number of extensions: 15 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: 255 Length adjustment: 25 Effective length of query: 250 Effective length of database: 230 Effective search space: 57500 Effective search space used: 57500 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: 47 (22.7 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