Align Glycolate permease, GlcA or YghK (substrates: L-lactate, D-lactate and glycolate) (characterized)
to candidate AO356_22315 AO356_22315 lactate permease
Query= TCDB::Q46839 (560 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_22315 Length = 587 Score = 503 bits (1295), Expect = e-147 Identities = 264/587 (44%), Positives = 364/587 (62%), Gaps = 32/587 (5%) Query: 2 VTWTQMYMPMGGLGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMP 61 + W Q+Y P G LS L+A +P++ +LA +K H+A + L ++LIAIFAF MP Sbjct: 1 MVWQQVYDPFGNAVLSTLLAAVPVVVMLASLAFFHVKAHLAALLALASALLIAIFAFGMP 60 Query: 62 IDMAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVISITDDQRLQVLLI 121 + MA +AA YG GL PI WI++ +FL++LT +G F +++ S+ ITDD+RLQ+LLI Sbjct: 61 VGMAGSAALYGAANGLLPIGWIVLNIIFLHRLTTENGSFKVLQDSLARITDDRRLQLLLI 120 Query: 122 GFSFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANTAPVAFGALGVPILVAG 181 F FGA EGAAGFG PVA+TGA+L+GLGF PL A+GL LIANTAPVAFGALG PI+ Sbjct: 121 AFCFGAFFEGAAGFGTPVAVTGAILIGLGFSPLAASGLALIANTAPVAFGALGTPIITLA 180 Query: 182 QVTGIDPFHIGAMAGRQLPFLSVLVPFWLVAMMDGWKGVKETWPAALVAGGSFAVTQFFT 241 +VTG+D + M GRQLPF SVLVPFWL+ GW+ + E WPA LVAG SFA+ QF Sbjct: 181 KVTGLDEMELSMMVGRQLPFFSVLVPFWLIWAFAGWRKMLEVWPAILVAGVSFAIPQFLV 240 Query: 242 SNYIGPELPDITSALVSIVSLALFLKVWRPKNTETAISM-----GQSAGAMVVNKPSSGG 296 SNY GP L D+ +AL+S+ L FLKVW+P T+ ++ A KP++ Sbjct: 241 SNYHGPMLVDVIAALISMACLTGFLKVWKPATVHTSAALSGRVDNSKIDASEDEKPTASA 300 Query: 297 PVPSEYSLGQIIRAWSPFLILTVLVTIWTMKPFKALF----------------------A 334 ++ + + RAW P++ILTV V W + FK LF Sbjct: 301 AFSND-ARPAVGRAWMPWIILTVFVFAWGTQGFKNLFDTRPALDPQTQSAKLDPQSKPMR 359 Query: 335 PGGAFYSLVINFQIPHLHQQVLKAAPIVAQPTPMDAVFKFDPLSAGGTAIFIAAIISIFI 394 +S ++ F +HQQ+ K P+V QP +AV+KF+ +A G+ IF+AAI+ + Sbjct: 360 EANPIFSPLVTFGT--IHQQIEKVPPVVPQPKTEEAVYKFNWFTATGSGIFLAAILGGLL 417 Query: 395 LGVGIKKGIGVFAETLISLKWPILSIGMVLAFAFVTNYSGMSTTLALVLAGTGVMFPFFS 454 +G I + + + TL +++ +++I +LA F+T YSG+ T+ L A TG+ +P F Sbjct: 418 MGYSIPQLVHHYLRTLWVVRYSLITIVAMLALGFLTRYSGLDATMGLAFAATGIFYPMFG 477 Query: 455 PFLGWLGVFLTGSDTSSNALFGSLQSTTAQQINVSDTLLVAANTSGGVTGKMISPQSIAV 514 LGWLGV LTGSDT+SN LFG LQ T++Q+ +S L+ AAN+SGGV GKM+ QSI V Sbjct: 478 TLLGWLGVALTGSDTASNVLFGGLQRVTSEQLGISPVLMAAANSSGGVMGKMVDAQSIVV 537 Query: 515 ACAATGMVGRESELFRYTVKHSLIFASVIGIITLLQAYV--FTGMLV 559 A AT G E E+ RY HS++ A ++G + LQAYV FT M+V Sbjct: 538 ASTATRWYGHEGEILRYVFFHSVVLAILVGGLVTLQAYVAPFTHMVV 584 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: 994 Number of extensions: 42 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: 587 Length adjustment: 36 Effective length of query: 524 Effective length of database: 551 Effective search space: 288724 Effective search space used: 288724 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