Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate BWI76_RS15030 BWI76_RS15030 ABC transporter
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__Koxy:BWI76_RS15030 Length = 263 Score = 167 bits (424), Expect = 2e-46 Identities = 93/213 (43%), Positives = 134/213 (62%), Gaps = 1/213 (0%) Query: 48 VNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREF 107 +ND+SL + G ++ I+G SG+GKSTL+R N L PTSG I+V+G DI ++D ALRE+ Sbjct: 19 LNDVSLQVPKGAVYGILGRSGAGKSTLIRCLNLLERPTSGRIIVNGNDITRMDKTALREY 78 Query: 108 RRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPH 167 R + M+FQ F LL +SV DN+A L++ K R + VGL +P Sbjct: 79 RL-RTGMIFQHFNLLHARSVADNIAVPLEIAKVPKAARQARVAELLELVGLADKAAAFPS 137 Query: 168 QLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITH 227 QLSGG +QRVG+ARALAA D++L DEA SALDP A + L ++ + L+ TIV ITH Sbjct: 138 QLSGGQKQRVGIARALAARPDVLLCDEATSALDPETTASVLSLLADINQQLNLTIVLITH 197 Query: 228 DLDEAVRIGNRIAILKDGKLIQVGTPREILHSP 260 +LD + + A+L+ G++I+ G ++L +P Sbjct: 198 ELDVVKTLCDHAALLEHGEIIESGRIADLLVAP 230 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: 166 Number of extensions: 4 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: 276 Length of database: 263 Length adjustment: 25 Effective length of query: 251 Effective length of database: 238 Effective search space: 59738 Effective search space used: 59738 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: 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