Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__ANA3:7024900 Length = 499 Score = 299 bits (765), Expect = 2e-85 Identities = 172/496 (34%), Positives = 282/496 (56%), Gaps = 5/496 (1%) Query: 14 VVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRF 73 ++E +++K + AL DVS+R+ GE HAL+G NGAGKSTLV ++TG + D G++ F Sbjct: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 Query: 74 SGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARA 133 G DA + ++ VYQ ++ +L+VA+NLF+ +P R G+I ++ M DARA Sbjct: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123 Query: 134 LLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRI 193 +L +K+D+ A D S+ +QL+ IAR ++ A+ ++LDEPTA LD E++ LF + Sbjct: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183 Query: 194 SELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGL 253 ++L+ +GV +FI+H L +VY+I +TVLR+ + I + LP+ +LIEAM G Sbjct: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243 Query: 254 AVADAAAR-GALPADTAVALELKELT-GADYEGVSFTVKRGEVVGLTGATSSGRTSVAEA 311 + D + + AV L L++++ + ++ TV +G+ VGL G SGR+ V A Sbjct: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303 Query: 312 IAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIAR 371 + GL G+I + G L +++ GI P+DR +G++ S+ EN + + Sbjct: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQA 363 Query: 372 VLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLV 431 +G + + ++ Q ID L I + + LSGGNQQKV++AR LA P +LV Sbjct: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423 Query: 432 LIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDLRTCDRVLVMFRGRVAAEFPA 491 L +PT G+D+ + ++ ++ + +EG ++LV S ELD+L +V+ R R A + Sbjct: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELS 483 Query: 492 GWQ---DHDLIASVEG 504 G + H + A EG Sbjct: 484 GAELTSQHVMQAIAEG 499 Lambda K H 0.318 0.134 0.377 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: 553 Number of extensions: 34 Number of successful extensions: 5 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: 510 Length of database: 499 Length adjustment: 34 Effective length of query: 476 Effective length of database: 465 Effective search space: 221340 Effective search space used: 221340 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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