Align The pmf-dependent citrate uptake system, Cit1 (characterized)
to candidate BWI76_RS16110 BWI76_RS16110 L-tartrate/succinate antiporter
Query= TCDB::Q6D017 (484 letters) >FitnessBrowser__Koxy:BWI76_RS16110 Length = 501 Score = 303 bits (775), Expect = 1e-86 Identities = 176/481 (36%), Positives = 259/481 (53%), Gaps = 22/481 (4%) Query: 12 LAMIVILVIAAFFWQMEPPAGLNPAAWHSAVIFVATIVCIVANVLPIGAIGIISITLFAL 71 L M + +++A + P GL P AWH IFV IV ++ LP IGI + + AL Sbjct: 23 LMMAMPIIVAVLLLFVPVPEGLPPYAWHYFAIFVGVIVGLIFEPLPGAVIGITGVVVIAL 82 Query: 72 TY-----------AAGDKTASGAIQTALSDLNSSLIWLIVVAFMIARGFIKTGLGRRIAL 120 A K A + + A+S +S +WLI AFM A G+ KT GRR+AL Sbjct: 83 CSQWLLFSPEQLAAPNFKLAGASFKWAVSGFGNSTVWLIFGAFMFAAGYDKTQFGRRLAL 142 Query: 121 QMIRLLGKRTLGLAYGLAFADLVLSPAMPSNTARCGGIIYPIADSLSRSFDSKPEDASRS 180 +++ LG+R+L L Y + FADL+L+P PSNTAR GG IYPI +L + SKP D S Sbjct: 143 ILVKYLGRRSLTLGYAITFADLLLAPFTPSNTARSGGTIYPIIANLPPLYGSKPNDPSAR 202 Query: 181 KIGTFLITCIGNVNDVTAAMFMTAYTGNLLAVKLAAN-AGVTITWGSWFLAALVPCLISL 239 +IG++L+ +T++MF++A NLLA+ L + G+ I+WG+WF+A L ++ + Sbjct: 203 RIGSYLMWVAITAACITSSMFLSALAPNLLALALVKSIVGINISWGTWFIAFLPLGILLI 262 Query: 240 AIVPLLVYWLTKPEIRHTPDAPKLAVAELAKMGSISRGEWLMAFTVILLLVLWIFGDRLG 299 +PLL YW PE++ + P A EL K+G +SR E L+ V L++WIF Sbjct: 263 LTMPLLAYWFYPPEVKVNDEVPLWAARELEKLGRLSRNEILLLVFVCFALMMWIFAAE-W 321 Query: 300 VDATTASFVGLSFLLLTGVLSWEDVKNEKGAWDTLIWFAALLMMANQLKKLGFTNWFGDL 359 ++ A+ + + +L TGVLSW D+ + K AW+T WFA L+ +A+ L GF W Sbjct: 322 IEPALAALLVIVLMLWTGVLSWNDITSNKAAWNTFAWFATLVALADGLSSTGFIAW---- 377 Query: 360 IGSNIGHLMQGTSWVLVLLLLNAAYFYTHYFFASGNAQIAALFAVFLGVGINLNIPAVPM 419 +G G LM G S + ++L A++ HY FAS A AL L + IP + M Sbjct: 378 LGKEGGALMSGISPGVATVVLLLAFYLLHYLFASTTAHTTALLPAMLTIA--STIPGMNM 435 Query: 420 -AFMLAFTSSLYCS--LTQYTHARGPILFGAGYVPTAVWWRTGFVVSLVNQAIFMGAGLL 476 F+L +SL +T Y PI +G+GY+PT +WR G + + A + G Sbjct: 436 QVFVLLMVTSLGVMGIITPYGTGPSPIYYGSGYLPTKDYWRLGTIFGAIFLAALLLIGYP 495 Query: 477 W 477 W Sbjct: 496 W 496 Lambda K H 0.327 0.139 0.440 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: 939 Number of extensions: 57 Number of successful extensions: 7 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: 484 Length of database: 501 Length adjustment: 34 Effective length of query: 450 Effective length of database: 467 Effective search space: 210150 Effective search space used: 210150 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