Align Monocarboxylic acid transporter (characterized)
to candidate Echvi_1267 Echvi_1267 probable sodium:solute symporter, VC_2705 subfamily
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__Cola:Echvi_1267 Length = 567 Score = 155 bits (392), Expect = 4e-42 Identities = 136/512 (26%), Positives = 229/512 (44%), Gaps = 91/512 (17%) Query: 29 FIIVTMTVVLRVG----KSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGAIS 84 +I+V ++ L +G + +FY G S NG+A D++SAASF+ + G IS Sbjct: 8 YILVGLSFALYIGIAIWSRAGSTKEFYVAGGGVSPLANGMATGADWMSAASFISMAGLIS 67 Query: 85 LNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTLAV 144 GYDG +Y +G+ +++ LL+A LR G+FT+ D + R RV A + + Sbjct: 68 FMGYDGSVYLMGWTGGYVLLALLLAPYLRKFGKFTVPDFVGDRYYSNKARVVAVFCAIFI 127 Query: 145 TLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIKAV 204 + Y+ QM G G + S L++ V++G+ ++ Y +LGGMKG TY Q+ + Sbjct: 128 SFTYVAGQMRGVGIVFSRYLEVDIN--TGVIIGM--CIVFFYAVLGGMKGITYTQVAQYC 183 Query: 205 LLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILE--PGL----- 257 +L+ A M F+ + L ++ + + A D T +L+ G+ Sbjct: 184 VLI--FAFMVPAIFISMQ-----LTSNPIPQLGLGGTVA----DGTYLLDKLDGVLTDLG 232 Query: 258 --QYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFY- 314 Y + + D ++ LAL +GTAGLPHV++RF+TVP K+AR S +A+V I Y Sbjct: 233 FHAYTSGKKSMGDMFAITLALMVGTAGLPHVIVRFFTVPRVKDARLSAGYALVFIAILYT 292 Query: 315 ------------------------LMTLVLGYGAAALV---------------GPDR--- 332 L V + L+ P+R Sbjct: 293 TAPAVSAFGIYNAIDSVSEKPIDDLPEWVTNWQQTQLIKINDKNQDGVVQYVADPERNEF 352 Query: 333 -------VIAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAGLAITASAAVGH 385 V+A P A ++ G + AL +A AGL + S +V Sbjct: 353 TIDKDIMVLANPEIAQLPNWVVGLVAAGGMAAALSTA----------AGLLLVISTSVSR 402 Query: 386 DIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAFAVAASANL 445 D+ A N ++ +++ ++R+ V +++ G+ VA +VA AF +AA++ Sbjct: 403 DL--AKNFNPGISDKKELLIARVAAAVAVIVAGYFGV-NPPGFVAEVVAFAFGLAAASFF 459 Query: 446 PTILYSLYWKKFNTTGAVAAIYTGLISALLLI 477 P I+ ++ K+ N GA+ + GL+ L I Sbjct: 460 PVIIMGIFSKRMNKEGAIWGMLVGLVFTLSYI 491 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: 682 Number of extensions: 43 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 551 Length of database: 567 Length adjustment: 36 Effective length of query: 515 Effective length of database: 531 Effective search space: 273465 Effective search space used: 273465 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