Align Monocarboxylic acid transporter (characterized)
to candidate 8499545 DvMF_0315 SSS sodium solute transporter superfamily (RefSeq)
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__Miya:8499545 Length = 519 Score = 460 bits (1184), Expect = e-134 Identities = 254/532 (47%), Positives = 347/532 (65%), Gaps = 22/532 (4%) Query: 16 VGNP-ILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAA 74 +G P L+I F +F+ T+ V + + + +FY G S +G QNGLA+AGDY+SAA Sbjct: 9 IGQPNALSIGFFFLFVAFTLGVTWWAARRSRSAAEFYAAGRSVTGFQNGLALAGDYMSAA 68 Query: 75 SFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVR 134 SFLGI G ++L GYDG +YSIGF V W V + L+AEPLRN+G++T ADV+++RLRQ+P+R Sbjct: 69 SFLGIAGLVALKGYDGLIYSIGFLVGWPVMMFLIAEPLRNLGKYTFADVVAYRLRQRPIR 128 Query: 135 VAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKG 194 VAAACG+L FYLIAQM G+GSLV ++ + ++ V+ +VG VMIAYVL GGM Sbjct: 129 VAAACGSLMTVAFYLIAQMVGSGSLVHLMFGL---PYETAVL-VVGAVMIAYVLFGGMLA 184 Query: 195 TTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILE 254 TT+VQ+IKAVLL+GG ++M FV G + A + A+ ++L Sbjct: 185 TTWVQIIKAVLLLGGASVMVF--FVLRHFGFSP----------AELFRASAARYGDKVLA 232 Query: 255 PGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFY 314 PG ++ D +SL +AL GTAGLPH+LMRFYTVP AK ARKSV +A LI FY Sbjct: 233 PG----GLVSNPWDALSLGMALMFGTAGLPHILMRFYTVPDAKAARKSVFYATGLISYFY 288 Query: 315 LMTLVLGYGAAALVGPDRVIAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAG 374 ++T ++G+GA LVG + V N AA LLA GG++F+ I+AVAFAT+LAVVAG Sbjct: 289 VLTFIIGFGAMTLVGQEVVAGFDKGGNMAALLLAEVTGGTMFLGFIAAVAFATILAVVAG 348 Query: 375 LAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVA 434 L + + HD+Y V R GQSTE ++VR+++ V +G++++ LGI QNVAF+V Sbjct: 349 LTLAGATTYAHDLYANVFRRGQSTEDDEVRMAKRATVALGVLAVALGIAFKGQNVAFMVG 408 Query: 435 LAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGA 494 LAFA+AASAN P +L S+ WK+F+T GAV +I TG A+ LI LSP V D P Sbjct: 409 LAFAIAASANFPALLMSILWKRFSTFGAVCSIATGATLAVGLIVLSPTV-WVDVLHSPWG 467 Query: 495 DWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEMEVRSLTGVGVE 546 A F LKNP L+S+P AF AGW+G+++ + + AE ++R+ GVG E Sbjct: 468 MAAPFMLKNPALISLPAAFAAGWLGSVLRPEPDAEQRYAEQKIRNYLGVGAE 519 Lambda K H 0.324 0.138 0.393 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: 691 Number of extensions: 30 Number of successful extensions: 5 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: 551 Length of database: 519 Length adjustment: 35 Effective length of query: 516 Effective length of database: 484 Effective search space: 249744 Effective search space used: 249744 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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