Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate AZOBR_RS02940 AZOBR_RS02940 actetate permease
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__azobra:AZOBR_RS02940 Length = 572 Score = 180 bits (456), Expect = 2e-49 Identities = 150/492 (30%), Positives = 226/492 (45%), Gaps = 51/492 (10%) Query: 19 IGIAIWS--RAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVSFVGYDGSVY 76 +GI W+ R S K+FY AGGG+ NG+A A D+MSAASF+ +AG+V G+DG ++ Sbjct: 53 LGITYWAARRTKSAKDFYAAGGGITGFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIF 112 Query: 77 LMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAIFICFTYIAGQM 136 +GW G+ ++ +A LR GK+T D R+ RT+A ++ Y+ QM Sbjct: 113 SVGWLVGWPIILFLVAERLRNLGKYTFADVASYRFQQTPMRTMAACGSLATVTFYLIAQM 172 Query: 137 RGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVLIFAFMVPAIFI 196 G G + ++ V I ++ Y GGM T+ Q+ + +L+ Sbjct: 173 VGAGKLIQLLFGMDYLWAVVIVGVLMIAYVTFGGMLATTWVQIIKAVLLLSG-------- 224 Query: 197 SVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSA--QLGFSQYTEGSKGMIDVFF 254 + M +L + GF E A +T V + K G+ A L + S GM Sbjct: 225 ASFMAFAVLAKFGFSPE----AMFSTAVQVHPKATGIMAPGALITDPVSAISLGM----- 275 Query: 255 ITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPALAAFSRVNMIET 314 ALMFGTAGLPH+++RFFTV K+AR S +A FI Y L I Sbjct: 276 ---ALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFY----ILTFIIGFGAIVL 328 Query: 315 INGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGETN-EMKIDRDIMVLAT 373 + P++TG AY + K+ A G+ N M I M Sbjct: 329 LLAPDATG-AYPFL-------------------DAAKLAAAGGKPNPSMIIGGSNMAAIH 368 Query: 374 PEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNFMPD-ISDKQELLYA 432 A ++A A L+ AGL L +++VSHDL S+ E+ + Sbjct: 369 TAHAVGGDLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRASEHDEIRVS 428 Query: 433 RIAAALGIVMAGYFGIN-PPGFVAAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGM 491 +I + +++ + GI VA +V +AF +AAS+ FP ++M +F M GA+ G Sbjct: 429 KITTVIIGIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMTTRGAVLGG 488 Query: 492 VIGLLFSASYII 503 IGL+ S S +I Sbjct: 489 WIGLVSSVSLLI 500 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: 931 Number of extensions: 57 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: 572 Length adjustment: 36 Effective length of query: 536 Effective length of database: 536 Effective search space: 287296 Effective search space used: 287296 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