Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate 8499545 DvMF_0315 SSS sodium solute transporter superfamily (RefSeq)
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__Miya:8499545 Length = 519 Score = 172 bits (435), Expect = 4e-47 Identities = 145/504 (28%), Positives = 224/504 (44%), Gaps = 75/504 (14%) Query: 9 LIVGFTF---ALYIGIAIWS--RAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLA 63 L +GF F A +G+ W+ R+ S EFY AG V NG+A A D+MSAASF+ +A Sbjct: 15 LSIGFFFLFVAFTLGVTWWAARRSRSAAEFYAAGRSVTGFQNGLALAGDYMSAASFLGIA 74 Query: 64 GIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVC 123 G+V+ GYDG +Y +G+ G+ ++ +A LR GK+T D + R + R A Sbjct: 75 GLVALKGYDGLIYSIGFLVGWPVMMFLIAEPLRNLGKYTFADVVAYRLRQRPIRVAAACG 134 Query: 124 AIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYC 183 ++ Y+ QM G G + + +T V + AV+ Y + GGM T+ Q+ + Sbjct: 135 SLMTVAFYLIAQMVGSGSLVHLMFGLPYETAVLVVGAVMIAYVLFGGMLATTWVQIIKAV 194 Query: 184 VLIFAFMVPAIFISVMMTGHILPQLGFG-AELVDAAGNNTGVYLLEKLDGLSAQLGFSQY 242 +L+ V F +L GF AEL A+ G +L L + + Sbjct: 195 LLLGGASVMVFF--------VLRHFGFSPAELFRASAARYGDKVL-----APGGLVSNPW 241 Query: 243 TEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPA 302 S GM ALMFGTAGLPH+++RF+TVP K AR S +A I+ Y + Sbjct: 242 DALSLGM--------ALMFGTAGLPHILMRFYTVPDAKAARKSVFYATGLISYFY-VLTF 292 Query: 303 LAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGETNEM 362 + F + ++ + + ++K G Sbjct: 293 IIGFGAMTLV---------------GQEVVAGFDKGG----------------------- 314 Query: 363 KIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNFM-- 420 ++ L E+ + +AA A L+ AGL L +T+ +HDL F Sbjct: 315 ----NMAALLLAEVTG-GTMFLGFIAAVAFATILAVVAGLTLAGATTYAHDLYANVFRRG 369 Query: 421 PDISDKQELLYARIAAALGIVMAGYFGINPPG-FVAAVVAIAFGLAASSLFPAIIMGIFS 479 D + + R ALG V+A GI G VA +V +AF +AAS+ FPA++M I Sbjct: 370 QSTEDDEVRMAKRATVALG-VLAVALGIAFKGQNVAFMVGLAFAIAASANFPALLMSILW 428 Query: 480 RTMNKEGAIAGMVIGLLFSASYII 503 + + GA+ + G + I+ Sbjct: 429 KRFSTFGAVCSIATGATLAVGLIV 452 Lambda K H 0.326 0.140 0.423 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: 827 Number of extensions: 48 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 572 Length of database: 519 Length adjustment: 35 Effective length of query: 537 Effective length of database: 484 Effective search space: 259908 Effective search space used: 259908 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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