Align Monocarboxylic acid transporter (characterized)
to candidate AZOBR_RS02940 AZOBR_RS02940 actetate permease
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__azobra:AZOBR_RS02940 Length = 572 Score = 439 bits (1130), Expect = e-127 Identities = 247/556 (44%), Positives = 341/556 (61%), Gaps = 52/556 (9%) Query: 23 ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82 I +F+VF++ T+ + + T + DFY G +G QNGLAIAGDY+SAASFLGI G Sbjct: 42 IVMFLVFVLATLGITYWAARRTKSAKDFYAAGGGITGFQNGLAIAGDYMSAASFLGIAGL 101 Query: 83 ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142 + +G+DG ++S+G+ V W + L LVAE LRN+G++T ADV S+R +Q P+R AACG+L Sbjct: 102 VYTSGFDGLIFSVGWLVGWPIILFLVAERLRNLGKYTFADVASYRFQQTPMRTMAACGSL 161 Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202 A FYLIAQM GAG L+ +L + ++ W V IVG++MIAYV GGM TT+VQ+IK Sbjct: 162 ATVTFYLIAQMVGAGKLIQLLFGM-DYLWAVV---IVGVLMIAYVTFGGMLATTWVQIIK 217 Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGAT 262 AVLL+ G + M K + + AV+ H + T I+ P GA Sbjct: 218 AVLLLSGASFMAFAVLAKFGFSPEAMFSTAVQVHPKA----------TGIMAP----GAL 263 Query: 263 LTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVLGY 322 +T + ISL +AL GTAGLPH+LMRF+TV AKEARKSV +A IG FY++T ++G+ Sbjct: 264 ITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYILTFIIGF 323 Query: 323 GA-AALVGPDRVIAAP--------------------GAANAAAPLLAFELGGSIFMALIS 361 GA L+ PD A P G +N AA A +GG +F IS Sbjct: 324 GAIVLLLAPDATGAYPFLDAAKLAAAGGKPNPSMIIGGSNMAAIHTAHAVGGDLFFGFIS 383 Query: 362 AVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLG 421 AVAFAT+LAVVAGL + ++AV HD+Y +VI G+++E +++RVS+IT V+IG++SI LG Sbjct: 384 AVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRASEHDEIRVSKITTVIIGIVSIFLG 443 Query: 422 ILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSP 481 I QNVAF+V LAF +AASAN P +L S++W + T GAV + GL+S++ L+ + P Sbjct: 444 IAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMTTRGAVLGGWIGLVSSVSLLIMGP 503 Query: 482 AVSGNDSAMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEME----- 536 V + V G A+FP NPG+ +IPL+F+A W ++ DN E E Sbjct: 504 TVWKS----VLGNPAALFPYDNPGVFTIPLSFLAIWFFSIT---DNSKAAQDEREAYKAQ 556 Query: 537 -VRSLTGVGVEKAVDH 551 +RS TG+G E A H Sbjct: 557 YIRSQTGLGAEGASAH 572 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: 734 Number of extensions: 33 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: 572 Length adjustment: 36 Effective length of query: 515 Effective length of database: 536 Effective search space: 276040 Effective search space used: 276040 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