Align citrate transporter (characterized)
to candidate AO356_04915 AO356_04915 alpha-ketoglutarate permease
Query= CharProtDB::CH_014606 (431 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_04915 Length = 432 Score = 209 bits (533), Expect = 1e-58 Identities = 135/389 (34%), Positives = 207/389 (53%), Gaps = 27/389 (6%) Query: 13 AILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLMRPIGAVV 72 AI+ +SGN +E FDF+++ F A Y A FFP+++ L+ T VF +GFLMRPIG + Sbjct: 20 AIVGASSGNLVEWFDFYVYAFCAIYFAPAFFPSDNPTVQLVNTAGVFAAGFLMRPIGGWI 79 Query: 73 LGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQGFSAGVEL 132 G DR GR+ +MI++ +M G+LLIA +P Y+ IG+ APVL+L RLLQG S G E Sbjct: 80 FGRVADRHGRKNSMMISVLMMCFGSLLIACLPTYKDIGVWAPVLLLFARLLQGLSVGGEY 139 Query: 133 GGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDEISEWGWRIPFF 192 G + Y+SE+A G +GF+ S+Q + ++A + L L DE+ +GWRIPF Sbjct: 140 GTTATYMSEVALKGQRGFFASFQYVTLIGGQLLAVSLVVILQQFLNEDELRAYGWRIPFV 199 Query: 193 IGCMIIPLIFVLRRSLQETEAFLQRKHRP---------DTREIFTTIAKNWRIITAGTLL 243 +G + + LRRSL+ET + R+++ D + F T+ TAG L Sbjct: 200 VGAVAALISLFLRRSLKETSSKEMRENKDAGSIAALFRDHKAAFVTVLG----YTAGGSL 255 Query: 244 VAMTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRRPV 303 + FY T Y Y L A+ + + P+ G ++D+IGRR Sbjct: 256 I------FYTFTTYMQKYLVNTAGLHAKTASYIMTGALFLYMCMQPLFGMLADKIGRRNS 309 Query: 304 LMGITLLALVTTLPVMNWLTAAPD----FTRMTLVLLWFSFFFGMYNGAMVAALTEVMPV 359 ++ L + T+P++ L + F +TL L SF+ + +G + A E+ P Sbjct: 310 MLWFGGLGALCTVPILLTLKSISSPFLAFILITLALAIVSFYTSI-SGLVKA---EMFPP 365 Query: 360 YVRTVGFSLAFSLATAIFGGLTPAISTAL 388 VR +G LA+++A AIFGG ++ +L Sbjct: 366 EVRALGVGLAYAVANAIFGGSAEYVALSL 394 Lambda K H 0.328 0.141 0.432 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: 472 Number of extensions: 31 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: 431 Length of database: 432 Length adjustment: 32 Effective length of query: 399 Effective length of database: 400 Effective search space: 159600 Effective search space used: 159600 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 (21.8 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