Align histidine transport ATP-binding protein hisP (characterized)
to candidate WP_054655718.1 CES79_RS03450 amino acid ABC transporter ATP-binding protein
Query= CharProtDB::CH_003210 (257 letters) >NCBI__GCF_002217945.1:WP_054655718.1 Length = 247 Score = 240 bits (613), Expect = 2e-68 Identities = 123/249 (49%), Positives = 180/249 (72%), Gaps = 14/249 (5%) Query: 5 KLNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVV 64 K+ V +L K +G+++VLKG++++ + +V+ +IG SGSGKSTFLR +N LE P+ GSIV+ Sbjct: 6 KVKVSNLVKNFGDNKVLKGINMEVHDNEVVVVIGPSGSGKSTFLRNLNRLEAPTSGSIVI 65 Query: 65 NGQTINLVRDKDGQLKVAD-KNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGL 123 + + +AD K + +R + MVFQHFNL+S+++V ENVM AP+++ Sbjct: 66 D------------DMDIADPKTDINKVRENIGMVFQHFNLFSNLSVSENVMLAPVELKKK 113 Query: 124 SKQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSAL 183 +K+EA ++A L VG++ + LSGGQQQRV+IARALAM P V+LFDEPTSAL Sbjct: 114 TKEEATKQAHDLLNMVGLESKFNATVQ-SLSGGQQQRVAIARALAMNPNVMLFDEPTSAL 172 Query: 184 DPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNP 243 DPE+VG+VL +M+QLA++G TM+VVTHEMGFA+ V+ V+F+ G I+E+G P+++F +P Sbjct: 173 DPEMVGDVLAVMKQLAKQGMTMIVVTHEMGFAKEVADRVVFVDDGNIQEQGTPDEMFNHP 232 Query: 244 QSPRLQRFL 252 Q+P LQ FL Sbjct: 233 QNPHLQDFL 241 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: 190 Number of extensions: 4 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: 257 Length of database: 247 Length adjustment: 24 Effective length of query: 233 Effective length of database: 223 Effective search space: 51959 Effective search space used: 51959 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