Align histidine transport ATP-binding protein hisP (characterized)
to candidate Pf6N2E2_1800 putative ABC transporter ATP-binding protein
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1800 Length = 254 Score = 249 bits (635), Expect = 5e-71 Identities = 128/249 (51%), Positives = 182/249 (73%), Gaps = 6/249 (2%) Query: 6 LNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVN 65 + + L+K Y + LK ++++ G+V+ IIG SGSGKST LRC+N LEK +G + V+ Sbjct: 5 VKAVSLNKYYDQFHALKDINIEVEQGEVLCIIGPSGSGKSTLLRCVNQLEKIDKGGLWVD 64 Query: 66 GQTINLVRDKDGQLKVADKNQLRLLRTRLT--MVFQHFNLWSHMTVLENVMEAPIQVLGL 123 G+ LV + K+ + N+ ++ R RL+ MVFQ FNL+ HMTVL+N++E P QVL Sbjct: 65 GE---LVGYRIVGNKLHELNETQIARQRLSTGMVFQRFNLFPHMTVLQNIIEGPCQVLKR 121 Query: 124 SKQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSAL 183 S +EA E A++ LA+VG+ ++ + YP+ LSGGQQQRV+IARALAM P+++LFDEPTSAL Sbjct: 122 SPKEANEEALELLARVGLADK-RNSYPIELSGGQQQRVAIARALAMRPKLMLFDEPTSAL 180 Query: 184 DPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNP 243 DPELVGEVL +M+ LA+ G TM+VVTHE+GFAR VS ++F+ G+I E G+PE++ +P Sbjct: 181 DPELVGEVLSVMRDLAQTGMTMIVVTHELGFAREVSNRMVFMDGGQIVEAGSPEEILISP 240 Query: 244 QSPRLQRFL 252 Q+PR Q F+ Sbjct: 241 QNPRTQSFI 249 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: 203 Number of extensions: 7 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: 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