Align histidine transport ATP-binding protein hisP (characterized)
to candidate WP_057507327.1 ABB28_RS03690 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003210 (257 letters) >NCBI__GCF_001431535.1:WP_057507327.1 Length = 231 Score = 137 bits (345), Expect = 2e-37 Identities = 85/233 (36%), Positives = 130/233 (55%), Gaps = 18/233 (7%) Query: 6 LNVIDLHKRY---GEH-EVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGS 61 L + +HK Y GE VL+G+ L + + ++I G SGSGK+T + + L++PS GS Sbjct: 5 LELQQVHKHYAMAGEQVPVLRGIDLTIDRNEYVAITGPSGSGKTTLMNILGCLDRPSAGS 64 Query: 62 IVVNGQTINLVRDKDGQLKVADKNQLRLLRTR-LTMVFQHFNLWSHMTVLENVMEAPIQV 120 ++ GQ + + D+ ++ +R R + VFQ FNL S T L+N M P+ Sbjct: 65 YLLAGQPVTCL----------DEREMAGVRNRAIGFVFQSFNLMSRATALQNAMH-PLLY 113 Query: 121 LGLSKQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPT 180 + + E ++R + L KVG+ +RA G P LSGGQ+QRV+IARAL P +LL DEPT Sbjct: 114 RKMGRAERQQRGMDALCKVGLADRA-GHLPSQLSGGQRQRVAIARALCGSPSILLADEPT 172 Query: 181 SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEE 233 LD +++ + L +G T+V++THE A H VI + GK+ + Sbjct: 173 GNLDSATTRDIMALFDALWADGSTIVMITHETDIADHCH-RVIRIEDGKVSAD 224 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: 144 Number of extensions: 6 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: 231 Length adjustment: 24 Effective length of query: 233 Effective length of database: 207 Effective search space: 48231 Effective search space used: 48231 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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