Align Monocarboxylic acid transporter (characterized)
to candidate WP_097031687.1 CRO07_RS16135 cation acetate symporter
Query= SwissProt::Q8NS49 (551 letters) >NCBI__GCF_900207575.1:WP_097031687.1 Length = 554 Score = 395 bits (1014), Expect = e-114 Identities = 224/540 (41%), Positives = 327/540 (60%), Gaps = 30/540 (5%) Query: 20 ILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGI 79 ++ I++F+ F+ T+ + + T ++DFYT G +G QNGLAIAGDY+SAA+FLG+ Sbjct: 37 VIAIAMFLFFVAATLGLTAWAARRTKSASDFYTAGGGITGFQNGLAIAGDYMSAAAFLGV 96 Query: 80 VGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAAC 139 G + G DG Y++G+ V W + L ++AE LRN+GRFT ADV SFRL Q +R +A Sbjct: 97 SGMVFGKGVDGVFYTVGWTVGWPLILFMIAERLRNLGRFTFADVASFRLEQTRIRTLSAF 156 Query: 140 GTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQ 199 G L V +FYLIAQM GAG L+ +L + A V +VG++M+ YV GGM TT+VQ Sbjct: 157 GALTVVIFYLIAQMVGAGKLIQLLFGLE----YAYAVILVGVLMMLYVTFGGMLATTWVQ 212 Query: 200 MIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQY 259 + KAVLL+ G ++ +L ++ A++ HAA + IL P Sbjct: 213 ITKAVLLLSGCTLLVLLGLKHFGFSPEAMMQAAIDNHAAHE----------AILSP---- 258 Query: 260 GATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLV 319 ++++ + ISLALAL G AGLPH+LMRF+TVP AKEARKSV +A IG F+++ + Sbjct: 259 SSSISDPITAISLALALMCGPAGLPHILMRFFTVPDAKEARKSVFYATGFIGYFFMLAVT 318 Query: 320 LGYGAAALVGP-----DRVIAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAG 374 +G+ A LVG D G N AA L+ E+GG +F+ ISAVAFAT+LAVV+G Sbjct: 319 IGFLAITLVGTNPAYLDEAGKLLGGGNMAAIHLSGEVGGDVFLGFISAVAFATILAVVSG 378 Query: 375 LAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVA 434 LA++ ++AV HD+Y VI+ G++++ ++ VSR+ +V+G+++I LG++ QN+AF+V+ Sbjct: 379 LALSGASAVSHDLYARVIKKGRASDKTEMMVSRMATLVLGVLAIALGLVFENQNIAFMVS 438 Query: 435 LAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGA 494 LAF +AAS N P + S++WK T GA GL SA+ + L P V N V G Sbjct: 439 LAFGLAASVNFPVLFLSIFWKNMTTRGAFIGGLMGLFSAVGCVVLGPTVWVN----VLGF 494 Query: 495 DWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPD--NMDDLAAEME-VRSLTGVGVEKAVDH 551 + AIFP + L S+ AF W ++ + + +D + VRS TG+G AV H Sbjct: 495 ETAIFPWEQYALFSMTAAFGGIWFFSVTDRSERAKLDKAGFPAQFVRSETGLGAAGAVAH 554 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: 673 Number of extensions: 31 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: 554 Length adjustment: 36 Effective length of query: 515 Effective length of database: 518 Effective search space: 266770 Effective search space used: 266770 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 24 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