Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate Ga0059261_1053 Ga0059261_1053 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= uniprot:A0A1I1Y8J0 (492 letters) >FitnessBrowser__Korea:Ga0059261_1053 Length = 512 Score = 384 bits (986), Expect = e-111 Identities = 223/490 (45%), Positives = 292/490 (59%), Gaps = 55/490 (11%) Query: 28 TLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCYAE 87 +L R+L A L +LGIGA+IG GIFV+T +AA + AGP ++LSFV AG+ CA+AALCYAE Sbjct: 20 SLHRSLGAFQLTMLGIGAVIGTGIFVLTAEAA-QKAGPGMMLSFVIAGVVCAVAALCYAE 78 Query: 88 FAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALISGW 147 AAM+PVSGSAY+YSYA +GE +AW VGW+L+LEY V+ GWSGY ++ LI Sbjct: 79 MAAMVPVSGSAYTYSYAVMGELIAWMVGWALILEYAVAAGAVSVGWSGY---VVGLIENA 135 Query: 148 IGHDVSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFVNSIIV 207 D+ P L P+ DG I INLPA+ I +T L +G +SAFVNS++V Sbjct: 136 FALDI--PDALVRGPY---DGGI------INLPAMLIAGLVTWLLVIGTKESAFVNSVLV 184 Query: 208 AIKVTVILLFIAFATKYINPDNWHPFIPASEGASKYGWAGVGRAAAIVFFSYIGFDAVST 267 +KV+ + LFI A +N N+ PF P G+AGV AAA +FF+Y+GFDAVST Sbjct: 185 LVKVSALSLFIILAIPVMNMQNFEPFSP-------LGFAGVSAAAASIFFAYVGFDAVST 237 Query: 268 AAGEAKNPQRDMPIGIIGSLILCTILYIIV-AGILTGIADFRLLGTP----EPVSTALD- 321 AA E KNPQR+MPIG+IGSL +CTI Y++V AG++ + +LG P ST L Sbjct: 238 AAEETKNPQRNMPIGLIGSLAICTIFYLLVAAGVIGSVGAQPILGPDGAALPPGSTELTK 297 Query: 322 -----------------------NYPSLHWLQIIVVIGAVTGLS--SVMLVMLMGQPRIF 356 + W QI +IG GL+ SV+L+M+ GQ RIF Sbjct: 298 ACVETAAATGKEAVVCSKEALAWTLREIGWPQIGNLIGLAAGLALPSVILMMMFGQTRIF 357 Query: 357 YSMARDGLIPAVFGRIHQKFRTPHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFAT 416 + M+RDGL+PAVF ++H KF TPHV T++ GV A F +G L ++ GTL AFA Sbjct: 358 FVMSRDGLLPAVFSKVHPKFHTPHVITILTGVFVALFAAFFPVGKLADISNSGTLFAFAA 417 Query: 417 VCIGVLVLRYTRPELPRAFRVPVPWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQAI 476 V I VLVLR T P+ R FR P+ I P+ L C LF + + W A+G + Sbjct: 418 VSIAVLVLRRTDPDRKRPFRTPLIIITAPIAILGCAYLFYSLGHDTKMMFVGWAALGLLV 477 Query: 477 YFLYGYSHSK 486 YF GYS K Sbjct: 478 YF--GYSRRK 485 Lambda K H 0.328 0.141 0.441 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: 751 Number of extensions: 52 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 492 Length of database: 512 Length adjustment: 34 Effective length of query: 458 Effective length of database: 478 Effective search space: 218924 Effective search space used: 218924 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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