Align Histidine transport ATP-binding protein HisP (characterized)
to candidate 14789 b0652 glutamate and aspartate transporter subunit (NCBI)
Query= SwissProt::P02915 (258 letters) >FitnessBrowser__Keio:14789 Length = 241 Score = 221 bits (562), Expect = 1e-62 Identities = 119/243 (48%), Positives = 164/243 (67%), Gaps = 12/243 (4%) Query: 11 DLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNI 70 ++ K YG +VL S + + G+V+ + G SGSGKST ++ +N LE +G I V+G + Sbjct: 6 NVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVDGIVV 65 Query: 71 NLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDAR 130 N DK K L LR+R+ MVFQHF L+ H++++EN+ A ++VL K AR Sbjct: 66 N---DK--------KTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAR 114 Query: 131 ERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVG 190 E+ALK L +VG+ A K+P LSGGQQQRV+IARAL M+P +LFDEPTSALDPE++ Sbjct: 115 EKALKLLERVGLSAHAN-KFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMIN 173 Query: 191 EVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQ 250 EVL +M +LA EG TM+VVTHEMGFAR V++ VIF+ +GKI E+ + F +P+S R + Sbjct: 174 EVLDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAK 233 Query: 251 QFL 253 FL Sbjct: 234 DFL 236 Lambda K H 0.319 0.136 0.383 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: 179 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: 258 Length of database: 241 Length adjustment: 24 Effective length of query: 234 Effective length of database: 217 Effective search space: 50778 Effective search space used: 50778 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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