Align Monocarboxylic acid transporter (characterized)
to candidate WP_093426893.1 BM272_RS00985 cation acetate symporter
Query= SwissProt::Q8NS49 (551 letters) >NCBI__GCF_900112605.1:WP_093426893.1 Length = 604 Score = 149 bits (376), Expect = 3e-40 Identities = 92/304 (30%), Positives = 151/304 (49%), Gaps = 19/304 (6%) Query: 27 VVFIIVTMTVVLRVG----KSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82 +++++V T L +G + +FY G NG A A D++SAASF+ + G Sbjct: 6 LIYLVVGATFALYLGIAFWAKAGSTGEFYIAGGGVHPVANGAATAADWMSAASFISMAGL 65 Query: 83 ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142 I+ GYDG +Y +G+ +++ LL+A LR G+FT+ + + R RV A + Sbjct: 66 IAFLGYDGSVYLMGWTGGYVLLALLLAPYLRKFGKFTVPEFIGDRYYSDTARVVAVICLI 125 Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202 ++ Y+ QM G G + S L++ + +G+V Y +LGGMKG TY Q+ + Sbjct: 126 FISFTYVAGQMRGVGIVFSRFLEVELLTGLIIGMGVV----FVYAVLGGMKGITYTQVAQ 181 Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATK-----GYDPTQILEPGL 257 V+++ + V ++V+G N + +D A T D T + Sbjct: 182 YVVMIFAYTVPAVFIALQVTG------NPIPQVALGADLAGTSTDLLAKLDQTLVDLGFG 235 Query: 258 QYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMT 317 Y +D + LAL +GTAGLPHV++RF+TVP ++AR+S WA++ I Y Sbjct: 236 PYTEGSKPTVDVFFITLALMVGTAGLPHVIVRFFTVPKVRDARRSAGWALLFIALLYTTA 295 Query: 318 LVLG 321 +G Sbjct: 296 PAVG 299 Score = 66.6 bits (161), Expect = 3e-15 Identities = 53/185 (28%), Positives = 88/185 (47%), Gaps = 7/185 (3%) Query: 357 MALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLI 416 +AL++A A L+ AGL + S+A+ HD+ R Q +E ++ RI LI Sbjct: 413 IALVAAGGVAAALSTAAGLLLVISSAISHDLLKRTFRP-QISERGELAAGRIAAATAILI 471 Query: 417 SIVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLL 476 + LG VA +VA AF +AA++ P I+ ++ K+ N GA+A + GL+ L Sbjct: 472 AGYLGANPPAF-VAQVVAFAFGLAAASLFPVIIMGIFNKRMNREGAIAGMVVGLVFTLAY 530 Query: 477 IFLSPAVSGNDSAMVPGADWAIFPLKNPGL--VSIPLAFIAGWIGTLV--GKPDNMDDLA 532 I V A +W +F + G+ +++ L F W + V P ++ +L Sbjct: 531 IIYFKGVFVEPFAADVPENW-LFGISPEGIGGLAMLLNFAVAWTVSKVTAAPPQSIQELV 589 Query: 533 AEMEV 537 A + V Sbjct: 590 ASIRV 594 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: 710 Number of extensions: 43 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: 604 Length adjustment: 36 Effective length of query: 515 Effective length of database: 568 Effective search space: 292520 Effective search space used: 292520 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