Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_013402416.1 CALHY_RS02350 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >NCBI__GCF_000166355.1:WP_013402416.1 Length = 225 Score = 124 bits (312), Expect = 1e-33 Identities = 70/201 (34%), Positives = 117/201 (58%), Gaps = 11/201 (5%) Query: 4 VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63 + + + ++++ + + AL ++ ++ ++FV I+GPSG GKSTL+ I+ LD TSG Sbjct: 2 IELYDIYKIYKMGENE-VYALNGINLKINVHEFVAIVGPSGSGKSTLMNIIGCLDTPTSG 60 Query: 64 RVLLDGAPV---------EGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKE 114 +LDG V E ++ G VFQ++ L P LT +N+ L +G+P + + + Sbjct: 61 TYILDGHEVSRLNDNQLAEIRNSKIGFVFQNFNLIPQLTALENVELPLIYKGVPASMRHK 120 Query: 115 RAAYFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLM 174 A +A+V L H P++LSGG QQR AIARAL +P I+L DEP G LD+++ + Sbjct: 121 LAKEALARVSLEHRMHHRPRELSGGQQQRVAIARALVTNPAIILADEPTGNLDSKSGAEI 180 Query: 175 QELLLGIWEAERKTVLFVTHD 195 ++ + A+ T++ +THD Sbjct: 181 IQIFKEL-HAQGSTIVLITHD 200 Lambda K H 0.322 0.136 0.394 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: 103 Number of extensions: 3 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: 259 Length of database: 225 Length adjustment: 23 Effective length of query: 236 Effective length of database: 202 Effective search space: 47672 Effective search space used: 47672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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