Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate N515DRAFT_0722 N515DRAFT_0722 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= uniprot:A0A1I1Y8J0 (492 letters) >FitnessBrowser__Dyella79:N515DRAFT_0722 Length = 479 Score = 532 bits (1371), Expect = e-156 Identities = 262/489 (53%), Positives = 347/489 (70%), Gaps = 14/489 (2%) Query: 1 MLKNLFATTQISPASADLPGGGAHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAAA 60 ++++LFA + P A L + +L+R L + LV+LG+GA+IGAGIFVITGQAAA Sbjct: 3 LIRSLFA---VKPVEASLTA-----DDSLRRTLGLKELVVLGVGAVIGAGIFVITGQAAA 54 Query: 61 EHAGPAIVLSFVFAGIACALAALCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVL 120 EHAGPA+ LSFV AG+A ALAAL YAEFAAMLPVSGSAY Y+YAT GE +AWF+GW++V Sbjct: 55 EHAGPALTLSFVLAGLAAALAALSYAEFAAMLPVSGSAYVYAYATFGELLAWFIGWNVVA 114 Query: 121 EYLFTVATVAAGWSGYFNKLLALISGWIGHDVSLPQTLAAAPFTVVDGHIQATGMFINLP 180 EYL V++VA GWSGY LL + + +P LA AP + DGH++ TG +NLP Sbjct: 115 EYLLAVSSVAVGWSGYGVGLLKSLG------IEVPAALANAPLSFKDGHLELTGALLNLP 168 Query: 181 AVAIIAAITGLCYVGITQSAFVNSIIVAIKVTVILLFIAFATKYINPDNWHPFIPASEGA 240 A+ ++AA+T L Y G QS S++VA+KV V++LF+ +Y++P WHP++PA++G Sbjct: 169 ALLVVAALTALLYRGTRQSTMFASVVVALKVIVVVLFVVCGLQYVDPSLWHPYVPANQGG 228 Query: 241 SKYGWAGVGRAAAIVFFSYIGFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGI 300 YGWAGV RAA VF++YIGFDAV+TAA E +NPQR++P GI+ SL +CT+LYIIVA + Sbjct: 229 DHYGWAGVFRAATSVFYAYIGFDAVATAAQETRNPQRNVPAGILISLAICTVLYIIVAAV 288 Query: 301 LTGIADFRLLGTPEPVSTALDNYPSLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMA 360 LTG+ + L T EPV+TAL +P L WL+++ +GAV GL+SV+LVM +G RI YSMA Sbjct: 289 LTGLVPYPQLATAEPVATALAAHPPLAWLKLLTQVGAVAGLTSVILVMHLGLSRILYSMA 348 Query: 361 RDGLIPAVFGRIHQKFRTPHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIG 420 DGL+P FG +H++ RTPH T++VG + L +F + +LG++++MGTLLAFATVCIG Sbjct: 349 GDGLLPTFFGAVHERHRTPHRTTLLVGAVGGVLAAVFPLSLLGDLLSMGTLLAFATVCIG 408 Query: 421 VLVLRYTRPELPRAFRVPVPWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLY 480 VLVLR T P LPR FRVP VC LG L C L Q L +W + AW +G IY Y Sbjct: 409 VLVLRRTHPNLPRGFRVPAAPAVCTLGVLVCAFLLAQMNLGNWILLAAWTTLGMLIYIAY 468 Query: 481 GYSHSKLRK 489 GY HS +R+ Sbjct: 469 GYRHSLMRR 477 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: 768 Number of extensions: 25 Number of successful extensions: 4 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: 492 Length of database: 479 Length adjustment: 34 Effective length of query: 458 Effective length of database: 445 Effective search space: 203810 Effective search space used: 203810 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