Align histidine transport ATP-binding protein hisP (characterized)
to candidate Pf6N2E2_2962 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2962 Length = 254 Score = 350 bits (897), Expect = e-101 Identities = 172/253 (67%), Positives = 213/253 (84%), Gaps = 1/253 (0%) Query: 5 KLNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVV 64 KL + LHK YGEHEVLKGVSL+A GDVIS+IG+SGSGKSTFLRCINFLE+P++G++ + Sbjct: 3 KLTIEGLHKSYGEHEVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQPNDGAMSL 62 Query: 65 NGQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLS 124 +GQ I +++D+ G + VAD ++L+ +RTRL MVFQHFNLWSHMTVLEN+ AP +VLG+S Sbjct: 63 DGQPIQMIKDRHG-MHVADADELQRIRTRLAMVFQHFNLWSHMTVLENITMAPRRVLGVS 121 Query: 125 KQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALD 184 KQEA +RA +YL KVG+ R +YP LSGGQQQRV+IARALAMEPEV+LFDEPTSALD Sbjct: 122 KQEADDRARRYLDKVGLPARVAEQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALD 181 Query: 185 PELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQ 244 PELVGEVL+++Q LAEEG+TM++VTHEM FAR VS V+FLHQG +EEEG PE + GNP Sbjct: 182 PELVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSNQVLFLHQGLVEEEGRPEDVLGNPT 241 Query: 245 SPRLQRFLKGSLK 257 S RL++FL G+LK Sbjct: 242 SERLKQFLSGNLK 254 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: 233 Number of extensions: 2 Number of successful extensions: 2 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: 254 Length adjustment: 24 Effective length of query: 233 Effective length of database: 230 Effective search space: 53590 Effective search space used: 53590 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: 47 (22.7 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