Align ABC transporter related (characterized, see rationale)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 303 bits (775), Expect = 1e-86 Identities = 171/494 (34%), Positives = 280/494 (56%), Gaps = 7/494 (1%) Query: 5 LELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFL 64 ++L+ I+K Y GV AL+ V + GE L GENG+GKSTL+K+++G + G + Sbjct: 10 IDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIA 69 Query: 65 GEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNL-FLGYEPRRLGLIHFKKMYADARA 123 G+ P + AG+ ++Q+ +L PNL+VA+N+ F R L F+ + ARA Sbjct: 70 GQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARA 129 Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183 L + + ID+ A + +A +QL+AI R +A A+++++DEPT +L KEV+ L GI+ Sbjct: 130 ALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGII 189 Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243 LK +GVA++F++H L +V ++S+++ VLRNG+ + E +E L M GR + E Sbjct: 190 RMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDVPE 249 Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303 V L+ ++ + GS ++ + G+ +G+ GLLG GR+ V A Sbjct: 250 ------VPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKA 303 Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQA 363 +FGL D+GSI + G + L P A A I PEDR +G+ SI N+ + Sbjct: 304 LFGLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLD 363 Query: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423 +L T + A ++ +L++ PD + P++ LSGGNQQ+V LARWL+ P +L+ Sbjct: 364 AHTSGGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLI 423 Query: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELS 483 L+ P+ G+D+G+ A+I +IR L EG+ ++V S +L EL+A ++V+V+R+ + L Sbjct: 424 LNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDALE 483 Query: 484 GAELTSQHVMQAIA 497 G LT + +A Sbjct: 484 GTALTEDDLAHRLA 497 Lambda K H 0.319 0.136 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: 511 Number of extensions: 23 Number of successful extensions: 8 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: 499 Length of database: 498 Length adjustment: 34 Effective length of query: 465 Effective length of database: 464 Effective search space: 215760 Effective search space used: 215760 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: 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