Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate GFF2882 Psest_2938 transporter, SSS family
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__psRCH2:GFF2882 Length = 551 Score = 157 bits (396), Expect = 1e-42 Identities = 137/487 (28%), Positives = 223/487 (45%), Gaps = 67/487 (13%) Query: 16 ALYIGIAIWS--RAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVSFVGYDG 73 A +GI W+ R ST ++Y AGG + NG+A A D+MSAASF+ ++ +V GYDG Sbjct: 45 AFTMGITKWAAKRNTSTADYYTAGGSITGFQNGLAIAGDFMSAASFLGISALVYTSGYDG 104 Query: 74 SVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAIFICFTYIA 133 +Y +G+ G+ ++ MA LR GKFT D R R ++ ++ + Y+ Sbjct: 105 LIYSIGFLVGWPIILFLMAERLRNLGKFTFSDVASYRLGQTQIRLLSAFGSLIVVAFYLI 164 Query: 134 GQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVLIFAFMVPA 193 QM G G + ++ V + ++ Y + GGM T+ Q+ + +L+ A Sbjct: 165 AQMVGAGKLIQLLFGLDYYVAVVLVGVLMVMYVLFGGMLATTWVQIIKAVLLLSG----A 220 Query: 194 IFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFSQYTEGSKGMIDVF 253 F+++M+ + FG+ +A V + EK + + G I Sbjct: 221 SFMAIMVMKSV--GFDFGSLFAEA------VKIHEKGAQIMSPGGL------VSDPISAI 266 Query: 254 FITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPALAAFSRVNMIE 313 + ALMFGTAGLPH+++RFFTV K+AR S +A FI Y + + F + ++ Sbjct: 267 SLGLALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFY-ILTFIIGFGAILLVS 325 Query: 314 TINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGETNEMKIDRDIMVLAT 373 T PE V TG I G TN + I LA+ Sbjct: 326 T--NPEFKDV--------------TGAI--------------VGGTNMVAIH-----LAS 350 Query: 374 PEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDL----LKKNFMPDISDKQEL 429 NL + ++A A L+ AGL L +++VSHDL +K+ ++ E+ Sbjct: 351 AVGGNL---FLGFISAVAFATILAVVAGLTLAGASAVSHDLYACVIKQG---KAREEDEM 404 Query: 430 LYARIAA-ALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAI 488 ++ LG+V I +A +V +AF +AAS FP + + ++ + ++ GA+ Sbjct: 405 RVTKLTTLTLGVVAILLGIIFEKQNIAFMVGLAFSIAASCNFPVLFLSMYWKGLSTRGAL 464 Query: 489 AGMVIGL 495 G +GL Sbjct: 465 FGGSLGL 471 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: 890 Number of extensions: 60 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: 551 Length adjustment: 36 Effective length of query: 536 Effective length of database: 515 Effective search space: 276040 Effective search space used: 276040 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