Align Serine/threonine exchanger SteT (characterized)
to candidate N515DRAFT_4009 N515DRAFT_4009 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= SwissProt::O34739 (438 letters) >FitnessBrowser__Dyella79:N515DRAFT_4009 Length = 445 Score = 210 bits (535), Expect = 6e-59 Identities = 128/430 (29%), Positives = 217/430 (50%), Gaps = 6/430 (1%) Query: 3 TEDNGLKKEIGLLFALTLVIGTIIGSGVFMKPGAVLAYSGDSKMALFAWLLGGILTLAGG 62 T +G + + A +V+G IIG G+F+ PG + L W+ G+LTL G Sbjct: 4 TPASGYMRRLTSWDAAMIVVGGIIGGGIFLNPGIAAQRTESGLALLLVWVGAGVLTLIGA 63 Query: 63 LTIAEIGTQIPKTGGLYTYLEEVYGEFWGFLCGWVQIIIYGPAIIGALGLYFGSLMANLF 122 L AE+G + P GG Y YL E +G GFL GW +++ A+ F S + +F Sbjct: 64 LCYAELGARRPHAGGSYVYLREAFGSLAGFLFGWTMLLVIYSGSAAAVATIFASYASGVF 123 Query: 123 GWGSGLSKVIGIIAVLFLCVINIIGTKYGGFVQTLTTIGKLIPIACIIVFGLW--KGDQH 180 G G K + A++F+ IN+ G K G VQ L T+ KL+ +A ++V GL+ D Sbjct: 124 GLPPGTIKPLAAGALVFVAGINLFGLKLGAQVQNLFTLLKLLAVAVLVVCGLFLAGADGA 183 Query: 181 IFTAVNESISDMNFGAAILATLFAYDGWILLAALGGEMKNPEKLLPRAMTGGLLIVTAIY 240 A + + ++ F A L LFAY G+ L L GE++ P++ LPRA+ G+L V +Y Sbjct: 184 GVLASDPARGNVGFIGAALPVLFAYSGFTYLNNLAGEVREPQRTLPRALFFGMLAVIVVY 243 Query: 241 IFINFALLHILSANEIVTLGENATSTAATMLFGSIGGKLISVGIIVSIFGCLNGKVLSFP 300 +N A L +L ++ + + + +FG IG K+I++GI VS G N +++ Sbjct: 244 ALVNVAYLAVL-GHDGLARSNTPAADVMSRVFGPIGAKVIAIGIAVSTLGFCNITLVAGA 302 Query: 301 RVSFAMAERKQLPFAEKLSHVHPSFRTPWIAISFQIALALIMMLISNPDKLSEISIFMIY 360 RV M + F ++ +HP RTP +A+ A+ + + N +L + + F + Sbjct: 303 RVLQVMGDDGL--FFRNVARLHPRHRTPNVALLLLSGWAVFLAMAFNFGQLLDYATFGDW 360 Query: 361 IFYVMAFFAVFILRKRAKGEKRAYSVPLYPFMPILAIAGSFFVLGSTLITDTMSCGLSIL 420 + + +F R R KG + VP YP +P++ + +++ +TL+ + + + Sbjct: 361 LACAVGVVTIFWYRSRDKG-GADFRVPGYPVLPLIFVGVVGWIVVATLLAKPIQACIVLA 419 Query: 421 IGLAGLPVYY 430 + G+PV++ Sbjct: 420 VMAVGIPVFH 429 Lambda K H 0.328 0.145 0.437 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: 626 Number of extensions: 39 Number of successful extensions: 6 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: 438 Length of database: 445 Length adjustment: 32 Effective length of query: 406 Effective length of database: 413 Effective search space: 167678 Effective search space used: 167678 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: 51 (24.3 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