Align Monocarboxylic acid transporter (characterized)
to candidate WP_099018878.1 CCS90_RS07195 cation acetate symporter
Query= SwissProt::Q8NS49 (551 letters) >NCBI__GCF_002591915.1:WP_099018878.1 Length = 579 Score = 164 bits (416), Expect = 7e-45 Identities = 136/499 (27%), Positives = 212/499 (42%), Gaps = 69/499 (13%) Query: 38 LRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGAISLNGYDGFLYSIGF 97 + + + DFY G NG+A A D++SAASF+ + G I+ GYD +Y +G+ Sbjct: 21 IAIWSKAKNTGDFYVAGKGVHPIANGMATAADWMSAASFISMAGIIAFAGYDASVYLMGW 80 Query: 98 FVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAG 157 +++ LL+A LR G+FT+ + + R K R+ A + ++ Y+ QM G G Sbjct: 81 TGGYVLLALLLAPYLRKFGKFTVPEFIGDRYYSKTARIVAVVCLIIISFTYVAGQMRGVG 140 Query: 158 SLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLT 217 + S L++ + +GIV Y +LGGMKG TY Q+ + +L+ + V Sbjct: 141 IVFSRFLEVEIITGLLIGMGIV----FFYAVLGGMKGITYTQVAQYCVLIFAYMVPAVFI 196 Query: 218 FVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGATLTTQLDFISLALALC 277 ++ +G L E S + TK Q L Y + +D + AL Sbjct: 197 AIQATGNPIPQLAFGSEVVGESVHLLTKLDQIVQDL-GFTAYTEGSKSSIDVFFITAALM 255 Query: 278 LGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVLG----YGAAALVGPDRV 333 +GTAGLPHV++RF+TVP +ARKS WA+ I Y V+G + P V Sbjct: 256 VGTAGLPHVIVRFFTVPKVSDARKSAFWALFFITILYTTAPVVGALGRMNLIETIQPGEV 315 Query: 334 IAAPGAANAA-----------APLLAFE-------------------------------- 350 A G A LLAFE Sbjct: 316 GTASGNLEYANKPNWFTTWEKTGLLAFEDKNGDGRIQYYNDKNPNFKPTADSYGWQGNEL 375 Query: 351 -LGGSIFMALISAVA----FATVLAVVAGLAITASAAVG----------HDIYNAVIRNG 395 + I + +A + L G+A S A G HD+ ++ Sbjct: 376 TVDRDIMVLANPEIAQLPDWVIALIAAGGIAAALSTAAGLLLVISAAISHDLVKGIMVPN 435 Query: 396 QSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWK 455 S E +++ V R+ +++ LG VA +VALAF +AAS+ P IL ++ K Sbjct: 436 IS-EKKELMVGRVAAAFAIMVAGYLG-ANPPGFVAQVVALAFGLAASSLFPAILMGIFSK 493 Query: 456 KFNTTGAVAAIYTGLISAL 474 + N GA+A + G++ L Sbjct: 494 RANKAGAIAGMIVGIVFTL 512 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: 644 Number of extensions: 42 Number of successful extensions: 5 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: 579 Length adjustment: 36 Effective length of query: 515 Effective length of database: 543 Effective search space: 279645 Effective search space used: 279645 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