Align Monocarboxylic acid transporter (characterized)
to candidate WP_011781716.1 MVAN_RS22925 cation acetate symporter
Query= SwissProt::Q8NS49 (551 letters) >NCBI__GCF_000015305.1:WP_011781716.1 Length = 543 Score = 701 bits (1809), Expect = 0.0 Identities = 362/548 (66%), Positives = 440/548 (80%), Gaps = 6/548 (1%) Query: 4 TILLAQDAVSEGVGNPILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNG 63 T LLAQ +E +GNP+ NI +F +F++VTM VV+R K + + +F+TGG FSG QNG Sbjct: 2 TTLLAQ---TETIGNPVANIGIFSLFVVVTMIVVIRASKRNATADEFFTGGRGFSGPQNG 58 Query: 64 LAIAGDYLSAASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADV 123 +AIAGDYLSAASFLGI GAI++ GYDGFLYSIGF VAWLVALLLVAE LRN GRFTMADV Sbjct: 59 IAIAGDYLSAASFLGIAGAIAVYGYDGFLYSIGFLVAWLVALLLVAELLRNTGRFTMADV 118 Query: 124 LSFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVM 183 LSFRL+Q+PVR+AAA TL V+LFYL+AQMAGAG LV++LLDI+ Q+VV+ +VG++M Sbjct: 119 LSFRLKQRPVRLAAATNTLTVSLFYLLAQMAGAGGLVALLLDINSRTGQSVVIAVVGVLM 178 Query: 184 IAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAA 243 I YVL+GGMKGTT+VQ+IKAVLL+ G MTV+ K + +L A + S Sbjct: 179 IVYVLVGGMKGTTWVQIIKAVLLIAGAGFMTVMVLAKFGMNFSEILGSAQSAISGSTTTG 238 Query: 244 TKGYDPTQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSV 303 G D +L PG QYG +LT+Q++FISLA+AL LGTAGLPHVLMRFYTVPTAKEAR+SV Sbjct: 239 VAGRD---VLAPGAQYGGSLTSQINFISLAIALVLGTAGLPHVLMRFYTVPTAKEARRSV 295 Query: 304 TWAIVLIGAFYLMTLVLGYGAAALVGPDRVIAAPGAANAAAPLLAFELGGSIFMALISAV 363 WAI LIGAFYL TLVLGYGAAALVGPDR++ A G N+AAPLLAFELGG + + +ISAV Sbjct: 296 VWAIALIGAFYLFTLVLGYGAAALVGPDRILGAAGGVNSAAPLLAFELGGVVLLGVISAV 355 Query: 364 AFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGIL 423 AFAT+LAVVAGL ITASA+ HDIY +V+++ + TEAEQVRVSRIT VV+G+++I LGIL Sbjct: 356 AFATILAVVAGLTITASASFAHDIYASVMKSHKVTEAEQVRVSRITAVVLGVLAIGLGIL 415 Query: 424 AMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAV 483 A QN+AFLVALAFAVAA+ANLPTI+YSLYW++FNT GA+ ++Y GLIS ++LI SPAV Sbjct: 416 ANGQNIAFLVALAFAVAAAANLPTIIYSLYWRRFNTRGALWSMYGGLISTIVLIVFSPAV 475 Query: 484 SGNDSAMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEMEVRSLTGV 543 SG+ +AM+PGAD+A FPL NPG+VSIPLAFI G +GTL D +AAEMEVRSLTG+ Sbjct: 476 SGSKTAMIPGADFAWFPLANPGIVSIPLAFILGIVGTLTSPDDEDPKVAAEMEVRSLTGI 535 Query: 544 GVEKAVDH 551 G EKAV H Sbjct: 536 GAEKAVAH 543 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: 774 Number of extensions: 26 Number of successful extensions: 2 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: 543 Length adjustment: 36 Effective length of query: 515 Effective length of database: 507 Effective search space: 261105 Effective search space used: 261105 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 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