Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate N515DRAFT_2925 N515DRAFT_2925 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= uniprot:A0A1I1Y8J0 (492 letters) >FitnessBrowser__Dyella79:N515DRAFT_2925 Length = 480 Score = 540 bits (1391), Expect = e-158 Identities = 261/490 (53%), Positives = 345/490 (70%), Gaps = 13/490 (2%) Query: 1 MLKNLFAT-TQISPASADLPGGGAHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAA 59 MLK LFA T S A HG +L+R L + LGIGA+IG GIFV+TGQAA Sbjct: 1 MLKQLFARKTDFSDAD------DCHGGPSLRRTLGKWGITALGIGAVIGTGIFVVTGQAA 54 Query: 60 AEHAGPAIVLSFVFAGIACALAALCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLV 119 AEHAGPA+++SF+ A I ALCYAEFA ++P+SGS+YSY+YATLGE VAWF+GW++V Sbjct: 55 AEHAGPAVLISFMLAAICSGFTALCYAEFATLIPISGSSYSYAYATLGELVAWFIGWNMV 114 Query: 120 LEYLFTVATVAAGWSGYFNKLLALISGWIGHDVSLPQTLAAAPFTVVDGHIQATGMFINL 179 LEY + + VAA W+GYF LL + + LP L AP DGH+ TG +NL Sbjct: 115 LEYGISASAVAASWTGYFTSLLDHVG------IHLPVALTEAPLAFKDGHLVTTGHLLNL 168 Query: 180 PAVAIIAAITGLCYVGITQSAFVNSIIVAIKVTVILLFIAFATKYINPDNWHPFIPASEG 239 PAVAI+ A+T LCYVGI +S+ +N ++VA+KV +I++ + +Y++P NWHPFIPA + Sbjct: 169 PAVAIVLALTWLCYVGIRESSGLNVLMVALKVGLIIVVVVAGYRYVDPANWHPFIPAEQE 228 Query: 240 ASKYGWAGVGRAAAIVFFSYIGFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAG 299 KYGW+G+ R AA+VFF+YIGF+A STAA E KNPQ+D+P G + SL++CT+LY+ +A Sbjct: 229 PGKYGWSGIMRGAAMVFFAYIGFEATSTAAQECKNPQKDLPFGTLVSLVICTVLYLAMAA 288 Query: 300 ILTGIADFRLLGTPEPVSTALDNYPSLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSM 359 +LTG+ + LGT EPV TA+ N+P L WL+++V IGA+ GLSSV+LVM++ QPRIF M Sbjct: 289 VLTGLIPYTELGTSEPVVTAIRNHPELGWLRLVVEIGAMIGLSSVILVMIIAQPRIFMIM 348 Query: 360 ARDGLIPAVFGRIHQKFRTPHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCI 419 +RDGL+P VF RIH K RTPH+ TV+ G+ A L +F + +L ++ +MGTL+AF VC Sbjct: 349 SRDGLLPPVFNRIHPKHRTPHLNTVITGIGIAILAAVFPLDLLADLTSMGTLIAFVAVCA 408 Query: 420 GVLVLRYTRPELPRAFRVPVPWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFL 479 GVL+LRYT PELPR FRVP W VC G +C+AL +W M+ W AIG AIYF Sbjct: 409 GVLILRYTAPELPRLFRVPAAWFVCTAGVFSCLALLYFMAWFNWLLMIIWTAIGLAIYFG 468 Query: 480 YGYSHSKLRK 489 YG HS+LR+ Sbjct: 469 YGMRHSRLRR 478 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: 818 Number of extensions: 42 Number of successful extensions: 2 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: 480 Length adjustment: 34 Effective length of query: 458 Effective length of database: 446 Effective search space: 204268 Effective search space used: 204268 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