Align Monocarboxylic acid transporter (characterized)
to candidate WP_007154786.1 MDG893_RS15635 cation acetate symporter
Query= SwissProt::Q8NS49 (551 letters) >NCBI__GCF_000170835.1:WP_007154786.1 Length = 588 Score = 147 bits (371), Expect = 1e-39 Identities = 89/279 (31%), Positives = 142/279 (50%), Gaps = 7/279 (2%) Query: 38 LRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGAISLNGYDGFLYSIGF 97 + + ++DFY G NG AI D++SAASF+ + G I+ GY + +G+ Sbjct: 21 IAIWAKAGSTSDFYVAGGGVHPITNGAAIGADWMSAASFISMAGLIAAGGYANSTFLMGW 80 Query: 98 FVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAG 157 +++ +L+A LR G+FT+ + + R K R+ A + ++ Y+I QMAGAG Sbjct: 81 TGGYVLLAMLLAPYLRKFGKFTVPEFIGDRFYSKNARLVAVICLIVASVTYVIGQMAGAG 140 Query: 158 SLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLT 217 S L++ + + I IV+ Y +LGGMKG TY Q+ + +L+ I V Sbjct: 141 VAFSRFLEVD----ATMGLIIAAIVVFVYAVLGGMKGITYTQVAQYCVLITAYTIPAVFI 196 Query: 218 FVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGL-QYGATLTTQLDFISLALAL 276 ++++G L H S + I + G +Y A + +L+ + L L Sbjct: 197 SLQLTGNALPPLG-LFSTHVDSGMPILDKLNQV-ITDLGFNEYTADVDNKLNMVLFTLTL 254 Query: 277 CLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYL 315 +GTAGLPHV++RF+TVP +AR S WA+V I YL Sbjct: 255 MIGTAGLPHVIIRFFTVPKVADARWSAGWALVFIALLYL 293 Score = 67.4 bits (163), Expect = 1e-15 Identities = 42/123 (34%), Positives = 68/123 (55%), Gaps = 2/123 (1%) Query: 357 MALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLI 416 + LI+A A L+ AGL + S+AV HD+ I N TE ++ +RI++ V ++ Sbjct: 394 IGLIAAGGLAAALSTAAGLLLAISSAVSHDLIKGSI-NPNITEKGELMAARISMAVAIVV 452 Query: 417 SIVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLL 476 + LG A +VALAF +AA++ P ++ ++ K+ N GA+A + TGL L Sbjct: 453 ATYLGANP-PGFAAQVVALAFGIAAASLFPALMMGIFSKRVNNVGAIAGMLTGLAFTLSY 511 Query: 477 IFL 479 IF+ Sbjct: 512 IFV 514 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: 635 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 551 Length of database: 588 Length adjustment: 36 Effective length of query: 515 Effective length of database: 552 Effective search space: 284280 Effective search space used: 284280 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