Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate 3610175 Dshi_3556 Na+/solute symporter (RefSeq)
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__Dino:3610175 Length = 598 Score = 655 bits (1689), Expect = 0.0 Identities = 344/601 (57%), Positives = 431/601 (71%), Gaps = 32/601 (5%) Query: 1 MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60 MD TL ++VG +FALY GIAIW+RAGST EFY AG GV+PV+NGMATAADWMSAASFI Sbjct: 1 MDQTTLNIIVVGLSFALYFGIAIWARAGSTSEFYAAGRGVNPVVNGMATAADWMSAASFI 60 Query: 61 SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120 S+AG+++FVGY S +LMGWTGGYVL+AL +APYLRKFGKFTVP+FIGDR+YS AR V Sbjct: 61 SMAGLIAFVGYSNSSFLMGWTGGYVLMALLLAPYLRKFGKFTVPEFIGDRFYSTKARVVG 120 Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180 V+C I I TY+ GQM G GV FSRFLEV TG+ VVF YAVLGGMKGITYTQVA Sbjct: 121 VICLIVISTTYVIGQMTGAGVAFSRFLEVSSTTGLVTASCVVFVYAVLGGMKGITYTQVA 180 Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGN-NTGVYLLEKLDGLSAQLGF 239 QY VLI A+ +PAIFIS+ +TG+ +P LG + + A G G LL LDGL LGF Sbjct: 181 QYVVLIIAYTIPAIFISLQLTGNPIPGLGLFSNM--APGQVGAGEPLLVTLDGLLTDLGF 238 Query: 240 SQYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTT 299 + YT GS + F T +LM GTAGLPHVI+RFFTVP+V DAR+SAGW LVFIA++Y T Sbjct: 239 NAYTTGSSPFLMALF-TLSLMIGTAGLPHVIIRFFTVPRVADARISAGWTLVFIALLYLT 297 Query: 300 IPALAAFSRVNMIETI--NGPESTGVAYETAPD-----WIKNWEKTGLIKWDDKNNDGKI 352 PA+ A +R+N+ + + G + V E + W+ W++TGL+ W+DKN DG+I Sbjct: 298 APAVGAMARLNITDLMWPEGTQGEAVTIEMIQNDPEYAWMNTWQQTGLLGWEDKNGDGRI 357 Query: 353 YY--------------AKGETNEM-KIDRDIMVLATPEIANLPAWVIALVAAGGLAAALS 397 Y A + NE+ +RDI+VLA PEIANLP WVIAL+AAGG+AAALS Sbjct: 358 QYYNDANPSMTERAEAAGWQGNELTNFNRDILVLANPEIANLPGWVIALIAAGGIAAALS 417 Query: 398 TSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARIAAALGIVMAGYFGINPPGFVAAV 457 T+AGLLL IS+++SHDL+K F P IS+K ELL ARI+ A IV+A Y G+NPPGF A V Sbjct: 418 TAAGLLLAISSAISHDLIKTVFNPSISEKGELLAARISMAGAIVVATYLGLNPPGFAAQV 477 Query: 458 VAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFK--FVNPGDN-- 513 VA+AFGLAA++LFPA++MGIFS+ +N GA GM++GL+ + +Y+ + F PG N Sbjct: 478 VALAFGLAAATLFPALMMGIFSKRINASGATWGMLVGLISTCAYLFTYLGIFFVPGTNFL 537 Query: 514 --NASNWLFGISPEGIGMLGMIINFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAGEAHD 571 ASN+LFGI P G +G ++NFAVA +VS+ T PQ + D+VES+R P+GAG A D Sbjct: 538 EPTASNYLFGIPPTHFGPIGALLNFAVAILVSRATEEPPQEIQDLVESVRIPRGAGAAVD 597 Query: 572 H 572 H Sbjct: 598 H 598 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: 1057 Number of extensions: 33 Number of successful extensions: 6 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: 572 Length of database: 598 Length adjustment: 37 Effective length of query: 535 Effective length of database: 561 Effective search space: 300135 Effective search space used: 300135 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