Align Citrate:H+ symporter (characterized)
to candidate 16686 b2587 alpha-ketoglutarate transporter (NCBI)
Query= TCDB::P16482 (444 letters) >FitnessBrowser__Keio:16686 Length = 432 Score = 239 bits (611), Expect = 1e-67 Identities = 141/430 (32%), Positives = 229/430 (53%), Gaps = 17/430 (3%) Query: 13 TAPVRMMATAGGARIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTF 72 TA ++ ++ RI AI+ +SGN +E FDF+++ F + Y AH FFP+ + L+ T Sbjct: 7 TADSKLTSSDTRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTA 66 Query: 73 AVFGAGFLMRPIGAIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLL 132 VF AGFLMRPIG + G DK GR+K +++++ +M G+ +I +P Y+TIG WAP L Sbjct: 67 GVFAAGFLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPAL 126 Query: 133 VLIGRLLQGFSAGAELGGVSVYLAEIATPGRKGFYTSWQ----SGSQQVAIMVAAAMGFA 188 +L+ RL QG S G E G + Y++E+A GRKGFY S+Q G Q +A++V Sbjct: 127 LLLARLFQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVV----V 182 Query: 189 LNAVLEPSAISDWGWRIPFLFGVLIVPFIFILRRKLEETQEFTARRHHLAMRQVFATLLA 248 L +E +A+ +WGWRIPF G ++ LRR+L+ET + R A+++ +L Sbjct: 183 LQHTMEDAALREWGWRIPFALGAVLAVVALWLRRQLDETSQQETR----ALKEA-GSLKG 237 Query: 249 NWQVVIAGMMMVAMT---TTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLP 305 W+ A +M++ T + FY T Y + + A+ + + P Sbjct: 238 LWRNRRAFIMVLGFTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQP 297 Query: 306 VGGALSDRFGRRSVLIAMTLLALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAM 365 + GALSD+ GRR+ ++ LA P L+ L N S +++ I Y Sbjct: 298 LIGALSDKIGRRTSMLCFGSLAAIFTVPILSALQNVSSPYAAFGLVMCALLIVSFYTSIS 357 Query: 366 IPALTEIMPAEVRVAGFSLAYSLATAVFGGFTPVISTALIEYTGDKASPGYWMSFAAICG 425 E+ PA+VR G L+Y++A A+FGG ++ +L + G + + ++++ A+ Sbjct: 358 GILKAEMFPAQVRALGVGLSYAVANAIFGGSAEYVALSL-KSIGMETAFFWYVTLMAVVA 416 Query: 426 LLATCYLYRR 435 L + L+R+ Sbjct: 417 FLVSLMLHRK 426 Lambda K H 0.329 0.139 0.421 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: 511 Number of extensions: 24 Number of successful extensions: 4 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: 444 Length of database: 432 Length adjustment: 32 Effective length of query: 412 Effective length of database: 400 Effective search space: 164800 Effective search space used: 164800 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 (21.9 bits) S2: 51 (24.3 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