Align histidine transport ATP-binding protein hisP (characterized)
to candidate WP_069956878.1 BEN30_RS03080 amino acid ABC transporter ATP-binding protein
Query= CharProtDB::CH_003210 (257 letters) >NCBI__GCF_001746755.1:WP_069956878.1 Length = 253 Score = 234 bits (598), Expect = 1e-66 Identities = 130/251 (51%), Positives = 171/251 (68%), Gaps = 12/251 (4%) Query: 2 SENKLNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGS 61 +E + ++D++K YGE VLK ++L G+ I I G SGSGKST +RCIN LE+ +G Sbjct: 9 NELAVQLVDVNKWYGEFHVLKNINLNVTPGERIVICGPSGSGKSTMIRCINRLEEHQKGK 68 Query: 62 IVVNGQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVL 121 I+VNG I L D LK D+ +R + M FQHFNL+ H+TVLEN API V Sbjct: 69 IIVNG--IELTED----LKRIDE-----VRREVGMCFQHFNLFPHLTVLENCTLAPIWVR 117 Query: 122 GLSKQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTS 181 + K EA + A+ YL +V I E+A KYP LSGGQQQRV+IAR+L M P+++LFDEPTS Sbjct: 118 KMPKSEAVKIAMHYLERVKIPEQAD-KYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTS 176 Query: 182 ALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFG 241 ALDPE++ EVL +M +LAEEG TM+ VTHEMGFA+ V+ VIF+ G++ EE P + F Sbjct: 177 ALDPEMIKEVLDVMVELAEEGMTMLCVTHEMGFAKLVANRVIFMDAGQVVEENEPHEFFD 236 Query: 242 NPQSPRLQRFL 252 NPQ+ R + FL Sbjct: 237 NPQNDRTKLFL 247 Lambda K H 0.318 0.134 0.375 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: 182 Number of extensions: 7 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: 257 Length of database: 253 Length adjustment: 24 Effective length of query: 233 Effective length of database: 229 Effective search space: 53357 Effective search space used: 53357 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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