Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate Dsui_0290 Dsui_0290 SSS sodium solute transporter
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__PS:Dsui_0290 Length = 582 Score = 169 bits (427), Expect = 4e-46 Identities = 149/580 (25%), Positives = 249/580 (42%), Gaps = 69/580 (11%) Query: 15 FALYIGIAIW------SRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVSF 68 F ++ +W S+ + +FY AGGG+ NG+A A D+MSAASF+ ++ V Sbjct: 42 FGAFVLATLWITKWAASKTKTAADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVFA 101 Query: 69 VGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAIFIC 128 GYDG +Y +G+ G+ ++ MA LR GKFT D R+ + R +A + + Sbjct: 102 NGYDGLIYSIGFLVGWPIIMFLMAERLRNLGKFTFADVAAYRFQATPIRALAASGTLVVV 161 Query: 129 FTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVLI-- 186 Y+ QM G G + ++ V + ++ Y + GGM T+ Q+ + +L+ Sbjct: 162 AFYLIAQMVGAGQLIKLLFGLDYWMAVVLVGILMMVYVLFGGMTATTWVQIIKAVLLLSG 221 Query: 187 -----------FAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSA 235 + F A+F + L G A+ ++ + T E + +A Sbjct: 222 ASFMVFMVLAKYGFSPEALFADAVRIKTDLAAKGLLAKALETDPSATA----ETVAAAAA 277 Query: 236 QLGFSQYTEGS--KGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFI 293 G S GS K I ALMFGTAGLPH+++RFFTVP K+AR S WA +I Sbjct: 278 AKGQSIMGPGSFIKDPISAISFGMALMFGTAGLPHILMRFFTVPDGKEARKSVFWATTWI 337 Query: 294 AIMYTTIPALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIY 353 Y + + F + V T P+++ + G++K N I+ Sbjct: 338 GYFY-ILTFIIGFGAI-------------VLVGTNPEFL---DAKGVLK--GGGNMAAIH 378 Query: 354 YAKGETNEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHD 413 A + + ++A A L+ AGL L +++VSHD Sbjct: 379 LANAVGGNV--------------------FLGFISAVAFATILAVVAGLTLSGASAVSHD 418 Query: 414 LLKKNFM-PDISDKQELLYARI-AAALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFP 471 L F ++ E+ +++ ALGI+ +A +V++AF +AAS+ FP Sbjct: 419 LYASVFRHGNVDSATEMRVSKMTTVALGIIAVVLGIAFEKQNIAFMVSLAFAIAASANFP 478 Query: 472 AIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFK--FVNPGDNNASNWLFGISPEGIGM 529 + M + + +GA G +GL+ + + K +V+ N + + SP M Sbjct: 479 VLFMSVLWKDCTTKGAFYGGFLGLITAVVLTVLSKSIWVDILGNKTEIFPYA-SPALFSM 537 Query: 530 LGMIINFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAGEA 569 I + ++ + A + V + + IR G G A Sbjct: 538 AAGFIGIWLFSLMDRSEQAAKERVAYLDQEIRSETGIGAA 577 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: 924 Number of extensions: 53 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: 582 Length adjustment: 36 Effective length of query: 536 Effective length of database: 546 Effective search space: 292656 Effective search space used: 292656 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: 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