Align histidine transport ATP-binding protein hisP (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 138 bits (347), Expect = 2e-37 Identities = 90/251 (35%), Positives = 137/251 (54%), Gaps = 16/251 (6%) Query: 6 LNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVN 65 L++ LH Y +VL+G++L G++ +++G SG GK+T LR I L+ S GSI +N Sbjct: 4 LSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSIAIN 63 Query: 66 GQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSK 125 G+T++ DG +K + M+FQ + L+ H+TV +N++ V L K Sbjct: 64 GKTVSA----DGCFVAPEKRSIG-------MIFQDYALFPHLTVADNIL---FGVRQLDK 109 Query: 126 QEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDP 185 Q R + L+ V ++ + +YP LSGGQQQRVSIARALA EP++LL DEP S +D Sbjct: 110 QSRSVRLEEMLSLVKLEGLGK-RYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDA 168 Query: 186 EL-VGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQ 244 ++ +L I L + V VTH A + + G+I + G PE L+ +P Sbjct: 169 QVRRALMLEIRAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPN 228 Query: 245 SPRLQRFLKGS 255 +P + FL S Sbjct: 229 TPYVADFLGAS 239 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: 10 Number of successful extensions: 4 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: 341 Length adjustment: 26 Effective length of query: 231 Effective length of database: 315 Effective search space: 72765 Effective search space used: 72765 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