Align Monocarboxylic acid transporter (characterized)
to candidate GFF1743 PS417_08865 acetate permease
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__WCS417:GFF1743 Length = 552 Score = 434 bits (1117), Expect = e-126 Identities = 250/562 (44%), Positives = 344/562 (61%), Gaps = 47/562 (8%) Query: 8 AQDAVSEGVGNPILNIS---VFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGL 64 A DA++ V LN+S +FVVF+ T+ + K + D+Y G +G QNGL Sbjct: 20 AADALTGEVHKQPLNVSAIVMFVVFVGATLCITYWASKRNKSAADYYAAGGKITGFQNGL 79 Query: 65 AIAGDYLSAASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVL 124 AIAGDY+SAASFLGI + +GYDG +YSIGF V W + L L+AE LRN+G++T ADV Sbjct: 80 AIAGDYMSAASFLGISALVYTSGYDGLIYSIGFLVGWPIILFLIAERLRNLGKYTFADVA 139 Query: 125 SFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAGSLVSVL--LDIHEFKWQAVVVGIVGIV 182 S+RL Q +R +ACG+L V FYLIAQM GAG L+ +L LD H V V +VGI+ Sbjct: 140 SYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFGLDYH------VAVILVGIL 193 Query: 183 MIAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYA 242 M+ YVL GGM TT+VQ+IKAVLL+ G + M ++ V+ L ++A++ H + Sbjct: 194 MVLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNALFSEAIKVHPKGE-- 251 Query: 243 ATKGYDPTQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKS 302 I+ P G + + SL LAL GTAGLPH+LMRF+TV AKEARKS Sbjct: 252 --------AIMSP----GGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKS 299 Query: 303 VTWAIVLIGAFYLMTLVLGYGAAALVG-----PDRVIAAPGAANAAAPLLAFELGGSIFM 357 V +A IG FY++T ++G+GA LV D A G N AA LA +GGSIF+ Sbjct: 300 VFYATGFIGYFYILTFIIGFGAILLVSTNPAFKDAAGALMGGNNMAAVHLANAVGGSIFL 359 Query: 358 ALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLIS 417 ISAVAFAT+LAVVAGL + ++AV HD+Y +VI+ G++ + +++RVS+IT + +G+++ Sbjct: 360 GFISAVAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANDKDEIRVSKITTIALGVLA 419 Query: 418 IVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLI 477 I LGIL +QN+AF+V LAF++AAS N P +L S+YWK T GA+ + GL+SA+ L+ Sbjct: 420 IGLGILFESQNIAFMVGLAFSIAASCNFPVLLLSMYWKNLTTRGAMIGGWLGLVSAVGLM 479 Query: 478 FLSPAVSGNDSAMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEME- 536 L P + + + AIFP + P L S+ +AF+ W ++ K AAE E Sbjct: 480 VLGPTI----WVSILHHEKAIFPYEYPALFSMIIAFVGIWFFSITDKSS-----AAEKER 530 Query: 537 -------VRSLTGVGVEKAVDH 551 VRS TG+G AV H Sbjct: 531 ALYFPQFVRSQTGLGSSGAVSH 552 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: 705 Number of extensions: 33 Number of successful extensions: 8 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: 552 Length adjustment: 36 Effective length of query: 515 Effective length of database: 516 Effective search space: 265740 Effective search space used: 265740 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