Align histidine transport ATP-binding protein hisP (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 136 bits (342), Expect = 7e-37 Identities = 87/248 (35%), Positives = 134/248 (54%), Gaps = 16/248 (6%) Query: 6 LNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVN 65 L + +H Y +L+G+ L + G++ +++G SG GK+T L+ I L+ S+G I +N Sbjct: 4 LTIEQVHSDYQGQTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRISIN 63 Query: 66 GQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSK 125 G+ ++ + + R + M+FQ + L+ H+TV EN++ V GL K Sbjct: 64 GRLLS-----------GPETFVPSERREVGMIFQDYALFPHLTVAENIL---FGVKGLDK 109 Query: 126 QEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDP 185 + R + LA V + E G+YP LSGGQQQRVSIARALA EPE+LL DEP S +D Sbjct: 110 AARQARLGEMLALVKL-EGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDA 168 Query: 186 ELVGEVL-RIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQ 244 ++ GE++ I + L + G + V VTH A + + G I + G+ E L+ P Sbjct: 169 KVRGEMMVEIREILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPT 228 Query: 245 SPRLQRFL 252 + FL Sbjct: 229 DKYVAEFL 236 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: 229 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: 257 Length of database: 342 Length adjustment: 26 Effective length of query: 231 Effective length of database: 316 Effective search space: 72996 Effective search space used: 72996 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: 48 (23.1 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