Align Glycolate permease, GlcA or YghK (substrates: L-lactate, D-lactate and glycolate) (characterized)
to candidate 208810 DVU3284 L-lactate permease
Query= TCDB::Q46839 (560 letters) >MicrobesOnline__882:208810 Length = 543 Score = 541 bits (1393), Expect = e-158 Identities = 279/558 (50%), Positives = 373/558 (66%), Gaps = 17/558 (3%) Query: 2 VTWTQMYMPMGGLGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMP 61 + W Q Y P+ SALVA IP+ F LAV R KGHVA + +I++AI + MP Sbjct: 1 MNWIQNYDPLSSALGSALVAAIPLFILFYMLAVKRAKGHVAAFLGTTSAIVLAIAVWGMP 60 Query: 62 IDMAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVISITDDQRLQVLLI 121 + +A +A YG YGL+PI WI++ AV++Y +TV SG+F+II+ S+ +TDD+RLQ + I Sbjct: 61 VSLAASATLYGAAYGLFPIVWIVITAVWVYNMTVESGEFEIIKDSLARLTDDRRLQAIFI 120 Query: 122 GFSFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANTAPVAFGALGVPILVAG 181 F+FG+ +EG AGFG PVAIT ++LVGLGF PLYAAG+CLIANTAPVAFGA+G+PI+VAG Sbjct: 121 AFAFGSFIEGTAGFGTPVAITASMLVGLGFNPLYAAGICLIANTAPVAFGAIGIPIIVAG 180 Query: 182 QVTGIDPFHIGAMAGRQLPFLSVLVPFWLVAMMDGWKGVKETWPAALVAGGSFAVTQFFT 241 QVTG+D HI + GRQLPFLSV+VP WL M G+K E PA VAG FA +QF Sbjct: 181 QVTGLDTMHISQIVGRQLPFLSVIVPMWLCVTMCGFKRAMEVLPAVAVAGVCFAGSQFVF 240 Query: 242 SNYIGPELPDITSALVSIVSLALFLKVWRPKNTETAISMGQSAGAMVVNKPSSGGPVPSE 301 SNY GP LPDI SA+V+I+ L L L+VW+P T + + V S+ Sbjct: 241 SNYHGPTLPDIMSAIVTIIGLVLLLRVWKPATTWRFPGEAEVELSAV-----------SQ 289 Query: 302 YSLGQIIRAWSPFLILTVLVTIWTMKPFKALFAPGGAFYSLVINFQIPHLHQQVLKAAPI 361 YS G +IRAW P++IL V+V W + K + +S+ +++ P LH + K API Sbjct: 290 YSAGDVIRAWMPYIILAVMVFFWGLDGVKKVL---DGIFSVSVDW--PGLHNLIEKTAPI 344 Query: 362 VAQPTPMDAVFKFDPLSAGGTAIFIAAIISIFIL-GVGIKKGIGVFAETLISLKWPILSI 420 A+ P A +K + +SAGGTAI ++ ++++ ++ G K I T L++P+++I Sbjct: 345 AAKNAPYAAKYKLNLISAGGTAILLSGLLAVPVMPKYGFDKAIACLFRTFYQLRFPVVTI 404 Query: 421 GMVLAFAFVTNYSGMSTTLALVLAGTGVMFPFFSPFLGWLGVFLTGSDTSSNALFGSLQS 480 M+L A + NYSGMS+TL + TG +FPFF+P LGWLGVFLTGSDTSSNALFG +Q Sbjct: 405 AMILGLAQIMNYSGMSSTLGIAFTKTGWLFPFFAPLLGWLGVFLTGSDTSSNALFGGMQR 464 Query: 481 TTAQQINVSDTLLVAANTSGGVTGKMISPQSIAVACAATGMVGRESELFRYTVKHSLIFA 540 TA+ + V L VAAN+SGGVTGKMISPQSI+VA A+T MVG+E LFR+T+ HS+ Sbjct: 465 ATAEAVGVDPHLTVAANSSGGVTGKMISPQSISVATASTNMVGQEGSLFRFTLGHSIAMT 524 Query: 541 SVIGIITLLQAYVFTGML 558 + ++TLLQAY GML Sbjct: 525 LFVCVLTLLQAYPLKGML 542 Lambda K H 0.327 0.141 0.424 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: 845 Number of extensions: 28 Number of successful extensions: 4 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: 560 Length of database: 543 Length adjustment: 36 Effective length of query: 524 Effective length of database: 507 Effective search space: 265668 Effective search space used: 265668 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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