Align Glycolate permease, GlcA or YghK (substrates: L-lactate, D-lactate and glycolate) (characterized)
to candidate 207586 DVU2110 L-lactate permease
Query= TCDB::Q46839 (560 letters) >MicrobesOnline__882:207586 Length = 545 Score = 513 bits (1320), Expect = e-150 Identities = 266/556 (47%), Positives = 359/556 (64%), Gaps = 17/556 (3%) Query: 4 WTQMYMPMGGLGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMPID 63 WTQ+Y P + LSA+VA++P+ F LAV R KGHVA A L + + + MP Sbjct: 3 WTQVYDPFSNITLSAMVAMLPLAILFYMLAVRRAKGHVAAACGLAGAFAATVAVWGMPAG 62 Query: 64 MAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVISITDDQRLQVLLIGF 123 +A A YG GL+PI WI++ AV+LY +TV SG+F+II+SS+ +TDD+RLQ L I F Sbjct: 63 LAVNATLYGVAMGLFPIIWIVLTAVWLYNMTVESGEFEIIKSSLARLTDDRRLQALFIAF 122 Query: 124 SFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANTAPVAFGALGVPILVAGQV 183 +FGA LEG AGFG PVAIT A+L+GLGF P+YA G+CLIANTAPVAFGALG+P++VA QV Sbjct: 123 AFGAFLEGTAGFGTPVAITAAMLMGLGFSPVYAGGICLIANTAPVAFGALGIPVIVASQV 182 Query: 184 TGIDPFHIGAMAGRQLPFLSVLVPFWLVAMMDGWKGVKETWPAALVAGGSFAVTQFFTSN 243 +G+D + GRQLP S++VP W+ +M G+K E PA +VA F+ TQF ++ Sbjct: 183 SGLDTLTLSQYVGRQLPVFSLIVPLWMTVVMCGFKRTMEVMPAIVVASVCFSGTQFIFAD 242 Query: 244 YIGPELPDITSALVSIVSLALFLKVWRPKNTETAISMGQSAGAMVVNKPSSGGPVPSEYS 303 + GP LPD+ +A+V+IV L + L+ W+P T KP + + +S Sbjct: 243 WHGPTLPDVMAAIVTIVGLLVLLRFWKPART----------WHFADEKPEA-ATGETRHS 291 Query: 304 LGQIIRAWSPFLILTVLVTIWTMKPFKALFAPGGAFYSLVINFQIPHLHQQVLKAAPIVA 363 G+++RAW+P+ IL V V W + K +++F+ P LH + K APIV Sbjct: 292 TGEVLRAWAPYAILAVFVFFWGLGSVKTFLN-----NIFIMSFEWPGLHAAIAKTAPIVK 346 Query: 364 QPTPMDAVFKFDPLSAGGTAIFIAAIISIFIL-GVGIKKGIGVFAETLISLKWPILSIGM 422 P A F F+ +SAGGTAI A ++S+ ++ G G + G A T L++PIL+I M Sbjct: 347 ADAPYAAKFTFNLISAGGTAILFAGLLSVPVMPGYGYGRAFGCLARTCYQLRFPILTIVM 406 Query: 423 VLAFAFVTNYSGMSTTLALVLAGTGVMFPFFSPFLGWLGVFLTGSDTSSNALFGSLQSTT 482 +L A + NYSGMS+TL + TG +FPFF+P +GWLGVFLTGS+TSSNALFGS+Q T Sbjct: 407 ILGLAQLMNYSGMSSTLGIAFTHTGALFPFFAPIMGWLGVFLTGSNTSSNALFGSMQHAT 466 Query: 483 AQQINVSDTLLVAANTSGGVTGKMISPQSIAVACAATGMVGRESELFRYTVKHSLIFASV 542 A + V L VAAN +GGVTGKMISPQSI+VA A+T VG+E LFR+ +KHS+ V Sbjct: 467 ASAVGVDPYLTVAANATGGVTGKMISPQSISVATASTHTVGQEGALFRFALKHSIAMTLV 526 Query: 543 IGIITLLQAYVFTGML 558 I ++ LQAYV ML Sbjct: 527 ICVLVTLQAYVIPWML 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: 835 Number of extensions: 26 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: 545 Length adjustment: 36 Effective length of query: 524 Effective length of database: 509 Effective search space: 266716 Effective search space used: 266716 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