Align Glycolate permease, GlcA or YghK (substrates: L-lactate, D-lactate and glycolate) (characterized)
to candidate 8501398 DvMF_2129 L-lactate transport (RefSeq)
Query= TCDB::Q46839 (560 letters) >FitnessBrowser__Miya:8501398 Length = 551 Score = 542 bits (1396), Expect = e-158 Identities = 282/561 (50%), Positives = 373/561 (66%), Gaps = 15/561 (2%) Query: 2 VTWTQMYMPMGGLGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMP 61 + W Q Y P+ + LSALVA +P+ F LAV R KGH A A+ ++L+AI + MP Sbjct: 1 MNWVQNYDPLSNILLSALVAAVPLYVLFYMLAVRRAKGHFAAALGTTAAVLLAILVWGMP 60 Query: 62 IDMAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVISITDDQRLQVLLI 121 +++A A YG YGL+PI WI++ AV++Y +TV SG+F+II+ S+ +TDD+RLQ + I Sbjct: 61 VNLAVNATLYGAAYGLFPIVWIVITAVWIYNMTVESGEFEIIKDSLARLTDDRRLQAIFI 120 Query: 122 GFSFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANTAPVAFGALGVPILVAG 181 F+FG+ +EG AGFG PVAIT A+LVGLGF PLYAAG+CLIANTAPVAFGA+G+P++VAG Sbjct: 121 AFAFGSFIEGTAGFGTPVAITAAMLVGLGFNPLYAAGICLIANTAPVAFGAIGIPVIVAG 180 Query: 182 QVTGIDPFHIGAMAGRQLPFLSVLVPFWLVAMMDGWKGVKETWPAALVAGGSFAVTQFFT 241 QV+G+D HI + GRQLPFLS++VP WL M G+K E PA +VAG FA +Q+ Sbjct: 181 QVSGLDTMHISQIVGRQLPFLSIIVPLWLCVTMCGFKRSLEVLPAVIVAGVCFAGSQYAF 240 Query: 242 SNYIGPELPDITSALVSIVSLALFLKVWRPKNTETAISMGQSAGAMVVNKPSSGGPVPSE 301 SN+ GP LPDI SA+++I+ L L L+VW+P T ++ S PS Sbjct: 241 SNFHGPTLPDIMSAIITIIGLVLLLRVWKPATT-----------WHFPDETPSSLTGPSP 289 Query: 302 YSLGQIIRAWSPFLILTVLVTIWTMKPFKALF--APGGAFYSLVI-NFQIPHLHQQVLKA 358 YS G+IIRAW P++IL ++V W + K A G F L F P LH + K Sbjct: 290 YSFGEIIRAWMPYIILAIMVFFWGLPEIKPYLDGALGAGFTPLAAKGFAWPGLHNAIEKT 349 Query: 359 APIVAQPTPMDAVFKFDPLSAGGTAIFIAAIISIFIL-GVGIKKGIGVFAETLISLKWPI 417 APIVA P A+FK + +SA GTAI + ++ ++ G + I T+ L++PI Sbjct: 350 APIVAANAPYGAMFKLNIISAAGTAILFTGLAAVPMMPKYGYGQAIPCLFRTMHQLRFPI 409 Query: 418 LSIGMVLAFAFVTNYSGMSTTLALVLAGTGVMFPFFSPFLGWLGVFLTGSDTSSNALFGS 477 L+I M+L A + NYSGMS+T+ L TG +FPFFSP LGWLGVFLTGSDTSSNALF Sbjct: 410 LTIAMILGLAQIMNYSGMSSTMGLAFTKTGWLFPFFSPLLGWLGVFLTGSDTSSNALFSG 469 Query: 478 LQSTTAQQINVSDTLLVAANTSGGVTGKMISPQSIAVACAATGMVGRESELFRYTVKHSL 537 LQ TTA + + L VAAN+SGGVTGKMISPQSI+VA AAT MVG+E +LFR+T+ HS+ Sbjct: 470 LQRTTATSVGMDPHLAVAANSSGGVTGKMISPQSISVATAATKMVGQEGQLFRFTLWHSV 529 Query: 538 IFASVIGIITLLQAYVFTGML 558 + I ++T+LQAY ML Sbjct: 530 AMTAFICVLTMLQAYPLKWML 550 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: 904 Number of extensions: 35 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: 551 Length adjustment: 36 Effective length of query: 524 Effective length of database: 515 Effective search space: 269860 Effective search space used: 269860 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