Align ABC transporter related (characterized, see rationale)
to candidate Ga0059261_2250 Ga0059261_2250 ABC-type multidrug transport system, ATPase component
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Korea:Ga0059261_2250 Length = 307 Score = 110 bits (275), Expect = 7e-29 Identities = 79/243 (32%), Positives = 126/243 (51%), Gaps = 15/243 (6%) Query: 5 LELKQISKHYPGVK-ALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 +E++ +SK Y G K AL+DVS + G++ LLG NGAGKSTL+ ++ G +K G Sbjct: 6 IEIEGLSKVYQGGKQALDDVSFTVPRGQIFGLLGPNGAGKSTLINILAGLVNKTAGRASI 65 Query: 64 LGEP--QHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADA 121 G QH P +A++A I V QE+ P T + L + + GL K + Sbjct: 66 WGFDIDQH---PRNAKRA-IGIVNQEILFDPFFTPVETLEI-----QAGLYGVPKAQRRS 116 Query: 122 RAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181 +L L+ A S +++ + +A+ + S VLVLDEPTA +D + Q L+ Sbjct: 117 MELLRAVHLEDKAHAYSRTLSGGMKRRLMVAKAMVHSPPVLVLDEPTAGVDIELRQQLWA 176 Query: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAEL---PQPKLIEAMLG 238 + L +GV +V TH+L++ ++ DRI ++ +G+ I T EL Q K +E + Sbjct: 177 YVRSLNERGVTVVLTTHYLEEAEELCDRIAIINHGKLIANEPTRELVGKTQEKAVEVTVD 236 Query: 239 RSL 241 R + Sbjct: 237 RDI 239 Score = 64.3 bits (155), Expect = 6e-15 Identities = 54/228 (23%), Positives = 107/228 (46%), Gaps = 17/228 (7%) Query: 271 KGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDA 330 K ++ ++ TVP+GQ GL G G+G+S + N + GL +G + G ++ Q Sbjct: 19 KQALDDVSFTVPRGQIFGLLGPNGAGKSTLINILAGLVNKTAGRASIWG--FDIDQHPRN 76 Query: 331 ISAGIALCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQEI--AQFFIDKLQ 388 I + ++ D P+ L +QA + + + R E+ A DK Sbjct: 77 AKRAIGIVNQEILFDPFFTPVE-----TLEIQAGL-YGVPKAQRRSMELLRAVHLEDK-- 128 Query: 389 IATPDADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCD 448 A LSGG ++++++A+ + P +LVLDEPT G+DI ++ +R+L + Sbjct: 129 -----AHAYSRTLSGGMKRRLMVAKAMVHSPPVLVLDEPTAGVDIELRQQLWAYVRSLNE 183 Query: 449 EGMSLLVASSELDELVAFSNKVVVLRDRYAVRELSGAELTSQHVMQAI 496 G+++++ + L+E +++ ++ + EL + +A+ Sbjct: 184 RGVTVVLTTHYLEEAEELCDRIAIINHGKLIANEPTRELVGKTQEKAV 231 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: 368 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 499 Length of database: 307 Length adjustment: 31 Effective length of query: 468 Effective length of database: 276 Effective search space: 129168 Effective search space used: 129168 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: 50 (23.9 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