Align Glycolate permease, GlcA or YghK (substrates: L-lactate, D-lactate and glycolate) (characterized)
to candidate H281DRAFT_00392 H281DRAFT_00392 lactate permease
Query= TCDB::Q46839 (560 letters) >FitnessBrowser__Burk376:H281DRAFT_00392 Length = 532 Score = 389 bits (999), Expect = e-112 Identities = 220/555 (39%), Positives = 329/555 (59%), Gaps = 30/555 (5%) Query: 6 QMYMPMGGLGL-SALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMPIDM 64 Q+ P+G L S LVA +PII + L R A LI+ +++AI ++ P+ + Sbjct: 4 QLLTPVGNSLLPSFLVAALPIIVVLLLLGWARRPAWQASLAGLIVGLVVAIAVWQFPVRL 63 Query: 65 AFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVI-SITDDQRLQVLLIGF 123 A + G ++ WP+ WI+ A+ LY + SG+F R +I ++ +D+R+ ++++GF Sbjct: 64 ALDSVAAGVVFACWPVMWIVFTAILLYNIAQRSGRFAAFRMWMIDNLPNDRRVVLVVVGF 123 Query: 124 SFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANTAPVAFGALGVPILVAGQV 183 SFGALLEG +GFG PVAIT +LL+ LGF L A LI NTAPVAFGALGVPI V G V Sbjct: 124 SFGALLEGISGFGTPVAITSSLLILLGFPTLEALTFTLIFNTAPVAFGALGVPITVLGAV 183 Query: 184 TGIDPFHIGAMAGRQLPFLSVLVPFWLVAMMDGWKGVKETWPAALVAGGSFAVTQFFTSN 243 T + + M GRQLPF ++L+PF+++A+ G++ + WP LV+G SFA+TQF SN Sbjct: 184 THLPADSLAKMVGRQLPFFALLLPFYVIAVYAGFRNMVRVWPVLLVSGASFALTQFVASN 243 Query: 244 YIGPELPDITSALVSIVSLALFLKVWRPKNTETAISMGQSAGAMVVNKPSSGGPVPSEYS 303 Y+ L D+ S++VS+V FL+VW+P + A ++ V K GG Sbjct: 244 YVNYSLTDVLSSMVSLVVTIAFLRVWKPA-VDPAFAVNIDRVGEVRGK--IGGS------ 294 Query: 304 LGQIIRAWSPFLILTVLVTIWTMKPFKALFAPGGAFYSLVINFQIPHLHQQVLKAAPIVA 363 + W P++I++V+V +WT+ A L+ + ++P + KA I Sbjct: 295 -----QGWYPWIIVSVVVIVWTV-----------AKIFLIGDVKVP--WPGLDKAVFITL 336 Query: 364 QPTPMDAVFKFDPLSAGGTAIFIAAIISIFILGVGIKKGIGVFAETLISLKWPILSIGMV 423 TP A++ F PL A GTAI +AAII+ ++G+ + +T + + IL++ + Sbjct: 337 YNTPYGAIWDFQPL-ATGTAILVAAIITSLVVGLSARDFGAAIVDTWVQTRIAILTVATI 395 Query: 424 LAFAFVTNYSGMSTTLALVLAGTGVMFPFFSPFLGWLGVFLTGSDTSSNALFGSLQSTTA 483 + A++ NYSG++ TL L +A G FP S FLGW+ VFL+GSDTS NALFG+LQ A Sbjct: 396 VGLAYLMNYSGLTYTLGLGVASVGPFFPLVSAFLGWVAVFLSGSDTSGNALFGNLQVVAA 455 Query: 484 QQINVSDTLLVAANTSGGVTGKMISPQSIAVACAATGMVGRESELFRYTVKHSLIFASVI 543 Q+N++ L+ A N+SGGV GKMISPQ+I+ A T + G+E +F T KHS++ ++ Sbjct: 456 NQLNLNPVLMAATNSSGGVMGKMISPQNISTGVATTDLKGKEGVVFAKTFKHSILLTVLL 515 Query: 544 GIITLLQAYVFTGML 558 GI+ LQ V GM+ Sbjct: 516 GILVWLQQNVLQGMI 530 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: 869 Number of extensions: 43 Number of successful extensions: 5 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: 532 Length adjustment: 35 Effective length of query: 525 Effective length of database: 497 Effective search space: 260925 Effective search space used: 260925 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: 52 (24.6 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