Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate AO356_09255 AO356_09255 glycine/betaine ABC transporter
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_09255 Length = 372 Score = 276 bits (707), Expect = 4e-79 Identities = 143/262 (54%), Positives = 193/262 (73%), Gaps = 1/262 (0%) Query: 9 IEVKNVFKIFGNRSKEALE-LIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMGLS 67 ++ +NV+KIFG + A++ +++Q TK ++L + CVVGV+++SL + GEIF IMGLS Sbjct: 13 VDCQNVWKIFGESAPAAMQAVVQQGLTKTRILQDYSCVVGVSNVSLQVRRGEIFCIMGLS 72 Query: 68 GSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQSFGLLPHKSV 127 GSGKSTL+R N+LI P+SG +LV G+D+ L LRE R I MVFQS LLP+++V Sbjct: 73 GSGKSTLIRLLNKLITPSSGKVLVKGKDLSTLSAAQLREVRARHIGMVFQSVALLPNRTV 132 Query: 128 LDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLARALAADT 187 L+N A+GL+V+G K + A + VGL + +YP +LSGGM+QRVGLARA+ AD Sbjct: 133 LENTAFGLEVQGIGKAERYKVAERALAKVGLSEWSQRYPSELSGGMQQRVGLARAITADP 192 Query: 188 DIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAILKDGKL 247 ++ILMDE FSALDPLIR ++QD+ +L K L K+ VFITHDLDEA+RIG+RIAI+KDG + Sbjct: 193 EVILMDEPFSALDPLIRRQLQDEFRQLTKELGKSAVFITHDLDEAIRIGDRIAIMKDGVI 252 Query: 248 IQVGTPREILHSPADEYVDRFV 269 IQVGT EI+ PAD+YV FV Sbjct: 253 IQVGTAEEIVLKPADDYVAEFV 274 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: 290 Number of extensions: 13 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: 372 Length adjustment: 28 Effective length of query: 248 Effective length of database: 344 Effective search space: 85312 Effective search space used: 85312 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