Align Citrate/succinate antiporter; Citrate carrier; Citrate transporter (characterized)
to candidate 17139 b3063 predicted tartrate:succinate antiporter (NCBI)
Query= SwissProt::P0AE74 (487 letters) >FitnessBrowser__Keio:17139 Length = 487 Score = 474 bits (1221), Expect = e-138 Identities = 211/471 (44%), Positives = 322/471 (68%) Query: 9 WKLLAPLVVMGVMFLIPVPDGMPPQAWHYFAVFVAMIVGMILEPIPATAISFIAVTICVI 68 W+ LAPL V+ ++ L+PVP G+ W YFAVF +IVG+ILEP+P ++ + ++I I Sbjct: 8 WRYLAPLAVIAIIALLPVPAGLENHTWLYFAVFTGVIVGLILEPVPGAVVAMVGISIIAI 67 Query: 69 GSNYLLFDAKELADPAFNAQKQALKWGLAGFSSTTVWLVFGAFIFALGYEVSGLGRRIAL 128 S +LLF ++LA P F ++L W ++GFS++ +WL+F AF+F GYE +GLGRRIAL Sbjct: 68 LSPWLLFSPEQLAQPGFKFTAKSLSWAVSGFSNSVIWLIFAAFMFGTGYEKTGLGRRIAL 127 Query: 129 FLVKFMGKRTLTLGYAIVIIDILLAPFTPSNTARTGGTVFPVIKNLPPLFKSFPNDPSAR 188 LVK MG RTL LGYA++ +++LAP TPSN+AR G ++P+I+NLPPL++S PND S+R Sbjct: 128 ILVKKMGHRTLFLGYAVMFSELILAPVTPSNSARGAGIIYPIIRNLPPLYQSQPNDSSSR 187 Query: 189 RIGGYLMWMMVISTSLSSSMFVTGAAPNVLGLEFVSKIAGIQISWLQWFLCFLPVGVILL 248 IG Y+MWM +++ ++S++F+T APN+L + + + +SW WFL LP+ ++L+ Sbjct: 188 SIGSYIMWMGIVADCVTSAIFLTAMAPNLLLIGLMKSASHATLSWGDWFLGMLPLSILLV 247 Query: 249 IIAPWLSYVLYKPEITHSEEVATWAGDELKTMGALTRREWTLIGLVLLSLGLWVFGSEVI 308 ++ PWL+YVLY P + ++V WA EL+ MG L RE ++GL++ +L LW+FG + I Sbjct: 248 LLVPWLAYVLYPPVLKSGDQVPRWAETELQAMGPLCSREKRMLGLMVGALVLWIFGGDYI 307 Query: 309 NATAVGLLAVSLMLALHVVPWKDITRYNSAWNTLVNLATLVVMANGLTRSGFIDWFAGTM 368 +A VG V+LML L ++ W DI +AWN LA+L+ +A GL +GFI WF + Sbjct: 308 DAAMVGYSVVALMLLLRIISWDDIVSNKAAWNVFFWLASLITLATGLNNTGFISWFGKLL 367 Query: 369 STHLEGFSPNATVIVLVLVFYFAHYLFASLSAHTATMLPVILAVGKGIPGVPMEQLCILL 428 + L G+SP ++ L++VFY Y FAS +A+T+ + P+++A +P +P+ C+++ Sbjct: 368 AGSLSGYSPTMVMVALIVVFYLLRYFFASATAYTSALAPMMIAAALAMPEIPLPVFCLMV 427 Query: 429 VLSIGIMGCLTPYATGPGVIIYGCGYVKSKDYWRLGAIFGVIYISMLLLVG 479 +IG+ LTPYATGP I YG GY+ + DYWRLGAIFG+I++ +L++ G Sbjct: 428 GAAIGLGSILTPYATGPSPIYYGSGYLPTADYWRLGAIFGLIFLVLLVITG 478 Lambda K H 0.328 0.142 0.453 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: 929 Number of extensions: 53 Number of successful extensions: 3 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: 487 Length of database: 487 Length adjustment: 34 Effective length of query: 453 Effective length of database: 453 Effective search space: 205209 Effective search space used: 205209 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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