Align Monocarboxylic acid transporter (characterized)
to candidate 209382 DVU0446 sodium/solute symporter family protein
Query= SwissProt::Q8NS49 (551 letters) >MicrobesOnline__882:209382 Length = 515 Score = 462 bits (1188), Expect = e-134 Identities = 254/533 (47%), Positives = 348/533 (65%), Gaps = 27/533 (5%) Query: 16 VGNP-ILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAA 74 +G P ++I F F+ T+ + + + +++FY G S +G QNGLA+AGDY+SAA Sbjct: 8 LGQPNAVSILFFFAFVAFTLAITWFAARRSRSASEFYAAGRSVTGLQNGLALAGDYMSAA 67 Query: 75 SFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVR 134 SFLGI G +SL GYDG +YSIGF V W + + L+AEPLRN+GR+T ADV+++RLRQKP+R Sbjct: 68 SFLGIAGLVSLKGYDGLIYSIGFLVGWPLMMFLIAEPLRNLGRYTFADVVAYRLRQKPIR 127 Query: 135 VAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKG 194 +AAACG+L FYLIAQM G+G+LV ++ I +++ VV VG +M+AYVL GGM Sbjct: 128 IAAACGSLMTVCFYLIAQMVGSGALVQLMFGI---RYEYAVVA-VGFIMMAYVLFGGMLA 183 Query: 195 TTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILE 254 TT+VQ+ KAVLL+GG M V+ + T L A KH E Sbjct: 184 TTWVQITKAVLLLGGATAMVVMVLAQFDYSPTRLFVTAAAKHG----------------E 227 Query: 255 PGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFY 314 L G ++ D ISL +AL GTAGLPH+LMRFYTVP A+ ARKSV +A LI FY Sbjct: 228 AMLAPGGLVSNPWDAISLGMALMFGTAGLPHILMRFYTVPDARAARKSVFYATGLISYFY 287 Query: 315 LMTLVLGYGAAALVGPDRVIAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAG 374 ++T ++G+GA LVGPD + N AAPLLA GG++F+ I+AVAFAT+LAVVAG Sbjct: 288 VLTFIIGFGAMMLVGPDAIRMFDKGGNMAAPLLAEVTGGTMFLGFIAAVAFATILAVVAG 347 Query: 375 LAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVA 434 L + + HD+Y V + GQS EA++VRV++ + +G+I+++LGI QNVAF+V Sbjct: 348 LTLAGATTFSHDLYANVFKGGQSNEADEVRVAKRATIALGVIAMLLGIAFKGQNVAFMVG 407 Query: 435 LAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGA 494 LAFA+AASANLP +L S+ W+ +TTGAV AI TG + A+ LI +SP V + V Sbjct: 408 LAFAIAASANLPALLLSIMWRGCSTTGAVWAIVTGGVLAVGLIIVSPTVWTD----VFHL 463 Query: 495 DWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAE-MEVRSLTGVGVE 546 A FPLKNP L+S+P AF+AG G+L+ +PD+ + + ++R+ GVG E Sbjct: 464 GTAPFPLKNPALLSMPAAFMAGIAGSLL-RPDSEESARFDAQKIRNYLGVGAE 515 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: 694 Number of extensions: 28 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: 515 Length adjustment: 35 Effective length of query: 516 Effective length of database: 480 Effective search space: 247680 Effective search space used: 247680 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