Align histidine transport ATP-binding protein hisP (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 192 bits (488), Expect = 8e-54 Identities = 115/247 (46%), Positives = 152/247 (61%), Gaps = 15/247 (6%) Query: 10 DLHKRY--GEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVNGQ 67 D+ K Y G H L GVSL AG+V +IG+SG+GKST +R IN LE PS G ++V+G Sbjct: 6 DVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVIVDGD 65 Query: 68 TINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKQE 127 + L VA LR LR R+ M+FQHFNL S TV +NV P+++ G E Sbjct: 66 DV-------AALGVAG---LRALRRRVGMIFQHFNLLSGKTVAQNVA-FPLKLAGRPAAE 114 Query: 128 ARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDPEL 187 + R + L +VG+ A GKYP LSGGQ+QRV IARALA P+VLL DE TSALDPE Sbjct: 115 VKARTAELLERVGLSAHA-GKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPET 173 Query: 188 VGEVLRIMQQLAEE-GKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQSP 246 ++L ++ L E G T+V++THEM R V V L G++ EEGA E++F +P S Sbjct: 174 TEQILDLIAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASD 233 Query: 247 RLQRFLK 253 +RF++ Sbjct: 234 TARRFVR 240 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: 188 Number of extensions: 8 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: 332 Length adjustment: 26 Effective length of query: 231 Effective length of database: 306 Effective search space: 70686 Effective search space used: 70686 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