Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate AO353_07265 AO353_07265 spermidine/putrescine ABC transporter ATP-binding protein
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__pseudo3_N2E3:AO353_07265 Length = 374 Score = 241 bits (615), Expect = 2e-68 Identities = 142/362 (39%), Positives = 204/362 (56%), Gaps = 20/362 (5%) Query: 4 VTLRNIRKAYD-ENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTI 62 V+ R ++K+YD EN +++D+NL+I GEF+ +GPSG GK+T + M+AG E + G++ + Sbjct: 15 VSFRGVQKSYDGENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILL 74 Query: 63 DGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKILH 122 G +N+V P KR I MVFQ+YAL+PHMT+ +N+AF L + G K ++ V+ ++ Sbjct: 75 AGRAINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRGLNKSDVSDRVKRVLSMVQ 134 Query: 123 IDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLHDE 182 +D R P QLSGGQ+QRVA+ RA+ +P++ L DEPL LD LR M++E LH Sbjct: 135 LDAFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQR 194 Query: 183 LKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMNFM 242 L T++YVTHDQ EA+T++D++ V G ++Q+ P LY P N FVA FIG + N + Sbjct: 195 LGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAPPRELYEKPKNTFVANFIG--ENNRL 252 Query: 243 EGVVQSVTHDGVTVRYETGETQRVAVEPAAV---KQGDKVTVGIRPEHLHVGMAEDG--- 296 G + S T D V GE VE AV K G+ VT+ IRPE + + + + Sbjct: 253 NGRLHSHTGDRCVVELGRGE----KVEALAVNVGKTGEPVTLSIRPERVSLNGSSESCVN 308 Query: 297 -ISARTMAVESLGDAAYLYAESSVAPDGL----IARIPPLERHTKGETQKLGATPEHCHL 351 S R LGD + E D IA + P G+ LG EH Sbjct: 309 RFSGRVAEFIYLGDHVRVRLEVCGKTDFFVKQPIAELDP--ALAVGDVVPLGWQVEHVRA 366 Query: 352 FD 353 D Sbjct: 367 LD 368 Lambda K H 0.320 0.135 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: 361 Number of extensions: 14 Number of successful extensions: 1 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: 369 Length of database: 374 Length adjustment: 30 Effective length of query: 339 Effective length of database: 344 Effective search space: 116616 Effective search space used: 116616 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 (21.8 bits) S2: 49 (23.5 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