Align Citrate/succinate antiporter; Citrate carrier; Citrate transporter (characterized)
to candidate 14895 b0770 predicted transporter (NCBI)
Query= SwissProt::P0AE74 (487 letters) >FitnessBrowser__Keio:14895 Length = 477 Score = 282 bits (722), Expect = 2e-80 Identities = 165/491 (33%), Positives = 267/491 (54%), Gaps = 26/491 (5%) Query: 5 KDNIWKLLAPLVVMGVMFLIPVPDGMPPQAWHYFAVFVAMIVGMILEPIPATAISFIAV- 63 K ++WKL+ L + ++ +P P G+ AW F +++A IVG++++P P + IAV Sbjct: 3 KKSLWKLILILAIPCIIGFMPAPAGLSELAWVLFGIYLAAIVGLVIKPFPEPVVLLIAVA 62 Query: 64 -TICVIGSNYLLFDAKELADPAFNAQKQALKWGLAGFSSTTVWLVFGAFIFALGYEVSGL 122 ++ V+G+ L+D AF L+G+SS T WLVF AF + + +GL Sbjct: 63 ASMVVVGN---------LSDGAFKTTAV-----LSGYSSGTTWLVFSAFTLSAAFVTTGL 108 Query: 123 GRRIALFLVKFMGKRTLTLGYAIVIIDILLAPFTPSNTARTGGTVFPVIKNLPPLFKSFP 182 G+RIA L+ +G TL LGY V +D++LAP TPSNTAR GG V P+I ++ S P Sbjct: 109 GKRIAYLLIGKIGNTTLGLGYVTVFLDLVLAPATPSNTARAGGIVLPIINSVAVALGSEP 168 Query: 183 NDPSARRIGGYLMWMMVISTSLSSSMFVTGAAPNVLGLEFVSKIAGIQISWLQWFLCFLP 242 + S RR+G YLM + + T +S MF T A N+L L+ ++ I +QISW W L Sbjct: 169 -EKSPRRVGHYLMMSIYMVTKTTSYMFFTAMAGNILALKMINDILHLQISWGGWALAAGL 227 Query: 243 VGVILLIIAPWLSYVLYKPEITHSEEVATWAGDELKTMGALTRREWTLIGLVLLSLGLWV 302 G+I+L++ P + Y +Y PEI + T A L +G + RE L+G+ +L+L W+ Sbjct: 228 PGIIMLLVTPLVIYTMYPPEIKKVDN-KTIAKAGLAELGPMKIREKMLLGVFVLALLGWI 286 Query: 303 FGSEV-INATAVGLLAVSLMLALHVVPWKDITRYNSAWNTLVNLATLVVMANGLTRSGFI 361 F + ++ + V ++ ++ ML L +V W+D+ + WNTL+ ++ +++ L++ F Sbjct: 287 FSKSLGVDESTVAIVVMATMLLLGIVTWEDVVKNKGGWNTLIWYGGIIGLSSLLSKVKFF 346 Query: 362 DWFAGTMSTHLEGFSPNATVIVLVLVF--YFAHYLFASLSAHTATMLPVILAVGKGIPGV 419 +W A +L F + V V++F Y FAS SA+ MLPV A+ + G Sbjct: 347 EWLAEVFKNNL-AFDGHGNVAFFVIIFLSIIVRYFFASGSAYIVAMLPV-FAMLANVSGA 404 Query: 420 PMEQLCILLVLSIGIMGCLTPYATGPGVIIYGCGYVKSKDYWRLGAIFGVIYISMLLLVG 479 P+ + L+ S G +T Y G +I+G GY K +W +GA+ ++ + + +G Sbjct: 405 PLMLTALALLFSNSYGGMVTHYGGAAGPVIFGVGYNDIKSWWLVGAVLTILTFLVHITLG 464 Query: 480 ---WPILAMWN 487 W +L WN Sbjct: 465 VWWWNMLIGWN 475 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: 816 Number of extensions: 50 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: 487 Length of database: 477 Length adjustment: 34 Effective length of query: 453 Effective length of database: 443 Effective search space: 200679 Effective search space used: 200679 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