Align Monocarboxylic acid transporter (characterized)
to candidate RR42_RS06400 RR42_RS06400 acetate permease
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__Cup4G11:RR42_RS06400 Length = 546 Score = 409 bits (1052), Expect = e-118 Identities = 221/506 (43%), Positives = 317/506 (62%), Gaps = 27/506 (5%) Query: 13 SEGVGNPILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLS 72 S G G ++ I++F++F+ T+ V +S D Y G + QNG AIAGDY+S Sbjct: 26 SVGQGMNVIAIAMFLMFVAATLVVTRWAARSNHSVADHYAAGGKITALQNGWAIAGDYMS 85 Query: 73 AASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKP 132 AAS LGI + +GYDG +YSIGF +W + L L+AEPLRN+GRFT+ADV+S+RLRQ+P Sbjct: 86 AASLLGISALVFTSGYDGLIYSIGFLASWPIILFLIAEPLRNLGRFTLADVVSYRLRQRP 145 Query: 133 VRVAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGM 192 +R +A ++ + L YL++QM GAG LV +L F + A VV +VG++M+ YV GGM Sbjct: 146 IRAFSASSSIVIVLLYLVSQMVGAGKLVELLFG---FSYTAAVV-LVGVLMVVYVFFGGM 201 Query: 193 KGTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQI 252 TT++Q+IKAVLL+ G A M + + L L A+E H +AA I Sbjct: 202 LATTWIQIIKAVLLLAGAAFMAFMVMSRFGFSLNALFAQAIEAH--GKHAA--------I 251 Query: 253 LEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGA 312 + P G ++ + +SL LAL GTAGLPH+LMRF+TV K ARKS+ +A ++G Sbjct: 252 MRP----GGLVSDPVSAVSLGLALIFGTAGLPHILMRFFTVGDVKAARKSILYATGIVGI 307 Query: 313 FYLMTLVLGYGAAALVGPDRVIAAP-----GAANAAAPLLAFELGGSIFMALISAVAFAT 367 Y + +++G+G ALV D P G N A LA +GG++F+ I AVAF+T Sbjct: 308 GYALIIIIGFGTIALVASDPAYHTPAGAVIGGVNMVAVHLAHAVGGNLFLGFICAVAFST 367 Query: 368 VLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQ 427 +LAVVAGL + S+A+ HD+Y V+R G +T+ E++RVSR+T +V+G++SI+LGIL Q Sbjct: 368 ILAVVAGLTLAGSSAISHDLYAKVLRQGNATDKEEMRVSRMTTLVLGVLSILLGILFEKQ 427 Query: 428 NVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGND 487 +AF+V+L F++AAS+N P +L S+YW+ T GAV GL+SA++L LSP V Sbjct: 428 TIAFIVSLTFSIAASSNFPVLLLSIYWRGLTTRGAVVGGSLGLLSAVVLTVLSPTV---- 483 Query: 488 SAMVPGADWAIFPLKNPGLVSIPLAF 513 V G AI+P + P L S+ +AF Sbjct: 484 WVQVLGHARAIYPYEYPALFSMLVAF 509 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: 656 Number of extensions: 32 Number of successful extensions: 4 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: 546 Length adjustment: 36 Effective length of query: 515 Effective length of database: 510 Effective search space: 262650 Effective search space used: 262650 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