Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate HSERO_RS08545 HSERO_RS08545 glycine/betaine ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__HerbieS:HSERO_RS08545 Length = 377 Score = 186 bits (473), Expect = 5e-52 Identities = 93/227 (40%), Positives = 149/227 (65%), Gaps = 6/227 (2%) Query: 45 VVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDAL 104 V V+ +SL + GEI V +G SG GK+T ++ NRLI+PTSG +L++G+D +D Sbjct: 19 VKAVDAVSLKVAEGEICVFLGPSGCGKTTTLKMINRLINPTSGRVLLNGQDTSGIDEV-- 76 Query: 105 REFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGL--KGYE 162 E RRH I V Q GL P+ ++ +N+ ++ G K+ C ERA + V L K + Sbjct: 77 -ELRRH-IGYVIQQIGLFPNMTIEENITIVPRLLGWDKKRCQERATELMAMVALDPKKFL 134 Query: 163 NKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTI 222 +YP +LSGG +QR+G+ RALAAD ++LMDE F A+DP+ R +Q++ ++Q+ L+KT+ Sbjct: 135 KRYPRELSGGQQQRIGVIRALAADAPVLLMDEPFGAVDPINRESIQNEFFQMQRQLNKTV 194 Query: 223 VFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269 + ++HD+DEA+++G+++A+ + GKL+Q P +L P D++V FV Sbjct: 195 IMVSHDIDEAIKLGDKVAVFRAGKLVQFDNPDTLLARPKDDFVSAFV 241 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: 230 Number of extensions: 14 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: 377 Length adjustment: 28 Effective length of query: 248 Effective length of database: 349 Effective search space: 86552 Effective search space used: 86552 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 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