Align histidine transport ATP-binding protein hisP (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 149 bits (375), Expect = 1e-40 Identities = 89/248 (35%), Positives = 143/248 (57%), Gaps = 18/248 (7%) Query: 10 DLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVNGQTI 69 ++ K G +K +L N G++ I+G SGSGKST LRCIN L +P+ G +++NG I Sbjct: 32 EILKATGCTVAVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTDI 91 Query: 70 NLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKQEAR 129 KV+DK L++ R L MVFQ+F L H +VL N+ +++ G+ K E Sbjct: 92 ---------AKVSDKELLQIRRKELAMVFQNFGLLPHRSVLHNIAFG-LELQGVKKGERE 141 Query: 130 ERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDP---- 185 ++A++ + VG+ + + + LSGG QQRV +ARALA PEVLL DE SALDP Sbjct: 142 QKAMESMQLVGL-KGYENQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRV 200 Query: 186 ELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQS 245 ++ E+L + ++ KT+V +TH++ A + + + G+I + G E++ P + Sbjct: 201 QMQDELLTLQSKMK---KTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPAN 257 Query: 246 PRLQRFLK 253 ++RF++ Sbjct: 258 AYVERFVE 265 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: 243 Number of extensions: 11 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: 408 Length adjustment: 28 Effective length of query: 229 Effective length of database: 380 Effective search space: 87020 Effective search space used: 87020 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