Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_007695653.1 C447_RS15655 ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >NCBI__GCF_000336675.1:WP_007695653.1 Length = 332 Score = 179 bits (455), Expect = 5e-50 Identities = 93/224 (41%), Positives = 145/224 (64%), Gaps = 6/224 (2%) Query: 48 VNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREF 107 V+ + G V++G SG GK+T +R NRL +PT G I DG DI +L+ LR Sbjct: 18 VDGHDFEVEEGTTTVLVGPSGCGKTTTMRLVNRLEEPTEGTIYYDGTDIEELEATDLRR- 76 Query: 108 RRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGL--KGYENKY 165 +I V Q GL H +V +NVA +++G + A+R + +GL + + + Y Sbjct: 77 ---EIGYVIQDIGLFDHMTVGENVATVPELKGWEAERTADRVDELLELMGLPPEEFRDSY 133 Query: 166 PHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFI 225 P +LSGG +QRVG+ARALAA D++LMDE F ALDP+ R E+QD+ L++QK + TIVF+ Sbjct: 134 PGELSGGQQQRVGVARALAAGPDVMLMDEPFGALDPITREELQDEFLDIQKEIDTTIVFV 193 Query: 226 THDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269 THD++EA+++G++IA++ +GK++Q TP +L +P ++V+ F+ Sbjct: 194 THDINEALKMGDKIAVMNEGKVVQYDTPTALLDNPKTKFVEEFI 237 Lambda K H 0.321 0.138 0.387 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: 220 Number of extensions: 12 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: 276 Length of database: 332 Length adjustment: 27 Effective length of query: 249 Effective length of database: 305 Effective search space: 75945 Effective search space used: 75945 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: 48 (23.1 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