Align Monocarboxylic acid transporter (characterized)
to candidate Dsui_0522 Dsui_0522 SSS sodium solute transporter
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__PS:Dsui_0522 Length = 557 Score = 410 bits (1055), Expect = e-119 Identities = 245/570 (42%), Positives = 331/570 (58%), Gaps = 48/570 (8%) Query: 5 ILLAQDAVSEGVGNP---------ILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGA 55 +LLA A G G + I++FV F++ T+ + T + DFYT G Sbjct: 13 LLLAAGAAYAGPGTVGEAEKQPLNVAAIAMFVAFVLSTLGITYWAANRTKSTADFYTAGG 72 Query: 56 SFSGTQNGLAIAGDYLSAASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNV 115 +G QNGLAIAGDY+SAA+ LG+ + GYDGF+Y +GFFV W + L L+AE LRN+ Sbjct: 73 GITGFQNGLAIAGDYMSAATLLGLTSMVFAKGYDGFVYIVGFFVGWPIILFLMAERLRNL 132 Query: 116 GRFTMADVLSFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVV 175 GRFT AD+ S+RL Q VR AA +L V LFYLI QM GAG L+ +L + V Sbjct: 133 GRFTFADITSYRLDQSKVRTVAAISSLTVVLFYLITQMVGAGQLIKLLFGLD----YEVA 188 Query: 176 VGIVGIVMIAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEK 235 V +VG++M+ YV GGM TT+VQ+IKA LL+GG +M +L TL+ A E Sbjct: 189 VVVVGVLMMVYVTFGGMIATTWVQIIKACLLLGGGTLMMLLAMSHFGFDFETLVTKATEV 248 Query: 236 HAASDYAATKGYDPTQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPT 295 H D T+I+ P G+ L ++ +SL+L L GTAGLPH+LMRF+TVP Sbjct: 249 HK----------DGTKIMGP----GSLLADPVNAVSLSLGLMFGTAGLPHILMRFFTVPD 294 Query: 296 AKEARKSVTWAIVLIGAFYLMTLVLGYGAAALVGPDRVI--------AAPGAANAAAPLL 347 AK+ARKSV A IG F+L+ ++LG A LVG + G N A L Sbjct: 295 AKQARKSVFVATGFIGFFFLVVVLLGMSAIVLVGTNPEFFEGGNVGGKMIGGGNMVAMHL 354 Query: 348 AFELGGSIFMALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSR 407 A +GG+IF+ +SAVAFAT+LAVV+GLA+ ++A+ HDIY VI G+ +++VS+ Sbjct: 355 AKFVGGNIFLGFLSAVAFATILAVVSGLALAGASAISHDIYANVICKGKPKGGSELKVSK 414 Query: 408 ITVVVIGLISIVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIY 467 I + IGL +I LGI+ QN+AF+V LAF +AASAN P ++ S+YWK T GA+A Sbjct: 415 IASIFIGLAAIGLGIMFEKQNLAFMVGLAFGIAASANFPVLILSMYWKGLTTKGAIAGTI 474 Query: 468 TGLISALLLIFLSPAVSGNDSAMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDN 527 GL +A++ + LS AV V G AIFP P L S+PLAF+ I +V K D Sbjct: 475 CGLTAAVVFVVLSKAV----WVTVLGKAQAIFPYDQPALFSMPLAFL---IAFVVSKLDT 527 Query: 528 MDDLAAEME------VRSLTGVGVEKAVDH 551 E+E VR+ TG+G A +H Sbjct: 528 SAQAKREIEAFDDQYVRAQTGLGAAGASNH 557 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: 678 Number of extensions: 33 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: 551 Length of database: 557 Length adjustment: 36 Effective length of query: 515 Effective length of database: 521 Effective search space: 268315 Effective search space used: 268315 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: 53 (25.0 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