Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >NCBI__GCF_000191585.1:WP_013645374.1 Length = 223 Score = 130 bits (327), Expect = 2e-35 Identities = 74/180 (41%), Positives = 108/180 (60%), Gaps = 7/180 (3%) Query: 23 ALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRV------LLDGAPVEG-P 75 AL VD E+ + V+I+GPSG GKSTLL ++ GLD A G++ L+D + + Sbjct: 23 ALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDKANEGQISVAGVNLMDNSDLSNFR 82 Query: 76 GAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQ 135 E G VFQ + L P LT+ +N++ L + + + +ERA + V L P + Sbjct: 83 SNEIGFVFQLHNLIPNLTVLENVQIPLLGTDIDDKKMEERALKLLKSVNLENKVDQKPTK 142 Query: 136 LSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHD 195 LSGG +QR AIARAL N P I+L DEP GALD++T+ ++ +LLL I + E T++ VTH+ Sbjct: 143 LSGGERQRVAIARALVNHPSIILADEPTGALDSETQEVILKLLLDIHKKENVTLIMVTHE 202 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: 131 Number of extensions: 7 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: 223 Length adjustment: 23 Effective length of query: 236 Effective length of database: 200 Effective search space: 47200 Effective search space used: 47200 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 Apr 09 2024. 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