Align histidine transport ATP-binding protein hisP (characterized)
to candidate 200225 SO1042 amino acid ABC transporter, ATP-binding protein (NCBI ptt file)
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__MR1:200225 Length = 241 Score = 251 bits (640), Expect = 1e-71 Identities = 131/252 (51%), Positives = 179/252 (71%), Gaps = 12/252 (4%) Query: 6 LNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVN 65 +N+ +LHK YG++ VLKG++ G+V+S+IG SGSGKSTFLRCIN LE P++G I + Sbjct: 2 INITNLHKSYGDNAVLKGINEHIRQGEVVSVIGPSGSGKSTFLRCINLLENPTQGDIEIE 61 Query: 66 GQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSK 125 GQ+I KD DK LR ++ MVFQ+FNL+ H TVL+N+ AP+ + +++ Sbjct: 62 GQSITA---KDA---CVDK-----LRQKVGMVFQNFNLFPHKTVLQNITLAPVSLKLMTQ 110 Query: 126 QEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDP 185 EA +A+ L +VG+ ++A YP LSGGQ+QRV+IARALAMEP+++LFDEPTSALDP Sbjct: 111 AEADNKALALLTQVGLQDKANA-YPSSLSGGQKQRVAIARALAMEPDLMLFDEPTSALDP 169 Query: 186 ELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQS 245 E+VG+VL +M+ LA++G TMV+VTHEMGFAR VS VIF+ G + E PE+LF P+ Sbjct: 170 EMVGDVLDVMKDLAQKGMTMVIVTHEMGFARDVSDRVIFMDGGYVVESNIPEELFTRPKE 229 Query: 246 PRLQRFLKGSLK 257 R Q FL L+ Sbjct: 230 ARTQSFLSKVLR 241 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: 184 Number of extensions: 6 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: 241 Length adjustment: 24 Effective length of query: 233 Effective length of database: 217 Effective search space: 50561 Effective search space used: 50561 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