Align histidine transport ATP-binding protein hisP (characterized)
to candidate AZOBR_RS26405 AZOBR_RS26405 amino acid ABC transporter ATP-binding protein
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__azobra:AZOBR_RS26405 Length = 242 Score = 245 bits (625), Expect = 7e-70 Identities = 126/247 (51%), Positives = 174/247 (70%), Gaps = 12/247 (4%) Query: 6 LNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVN 65 +++ ++ K YG EVLKGVSL + G++++IIG SGSGKST LRCIN LE+ G+I V Sbjct: 4 VDIKNVTKSYGSIEVLKGVSLSIDEGEIVTIIGKSGSGKSTLLRCINALERIDGGAITVE 63 Query: 66 GQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSK 125 GQ++ D LR R R+ +VFQ FNL+ H+TV N+ API ++K Sbjct: 64 GQSVR-----------TDMPNLRGFRQRVGIVFQAFNLFPHLTVERNITLAPILNKRIAK 112 Query: 126 QEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDP 185 E R A+ LA+VG+ ++ YP LSGGQQQRV+IAR LAM P ++LFDE TSALDP Sbjct: 113 AEGRALALDVLARVGLADKIDA-YPAQLSGGQQQRVAIARCLAMGPHLMLFDEVTSALDP 171 Query: 186 ELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQS 245 ELVGEVL++M+ +A +G TMV+VTHEMGFAR+V++ ++F+HQG++ EEG P +LF NP++ Sbjct: 172 ELVGEVLKVMEDMARQGMTMVLVTHEMGFARNVASKIVFMHQGRVWEEGPPAELFANPRT 231 Query: 246 PRLQRFL 252 P L+ F+ Sbjct: 232 PELRSFI 238 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: 198 Number of extensions: 5 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: 242 Length adjustment: 24 Effective length of query: 233 Effective length of database: 218 Effective search space: 50794 Effective search space used: 50794 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: 46 (22.3 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