Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_011972867.1 MAEO_RS00720 ATP-binding cassette domain-containing protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000017185.1:WP_011972867.1 Length = 281 Score = 103 bits (256), Expect = 5e-27 Identities = 75/237 (31%), Positives = 119/237 (50%), Gaps = 21/237 (8%) Query: 21 GLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELAGKP--YEPTAV 78 G AL I++++G + L+GPNGAGK+T F G+ P +G L G P Y+ ++ Sbjct: 16 GTLALDRANISVEKGDMVALLGPNGAGKSTLFLHFNGILKPKSGKILLKGAPIKYDAKSL 75 Query: 79 HEVAKAGIARTFQNI--RLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKAEEAAIAK 136 EV K + FQN +LFA T ++V G G K EE + K Sbjct: 76 MEVRKT-VGIVFQNSDDQLFAP-TVKQDVAFGP-------------LNLGLKEEE--VEK 118 Query: 137 RAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMNATEKVQL 196 R +E L VG+ F + LS G ++R+ IA LA P+++ LDEP AG++ ++ Sbjct: 119 RVKEALKEVGMEGFENKPPHHLSGGQKKRVAIAGILAMHPEIMVLDEPTAGLDPMGASKI 178 Query: 197 RELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNEKVIEA 253 +L+ ++ + TI++ HDV LV +++ V+ K + G EV + K I + Sbjct: 179 MKLLYKLNKEGITIIISTHDVDLVPIYANKIFVMGKTKIVKSGTVEEVFSDIKTIRS 235 Lambda K H 0.319 0.137 0.384 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: 138 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: 260 Length of database: 281 Length adjustment: 25 Effective length of query: 235 Effective length of database: 256 Effective search space: 60160 Effective search space used: 60160 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 (21.7 bits) S2: 47 (22.7 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