Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate RR42_RS01695 RR42_RS01695 C4-dicarboxylate transporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Cup4G11:RR42_RS01695 Length = 433 Score = 516 bits (1328), Expect = e-151 Identities = 257/425 (60%), Positives = 333/425 (78%) Query: 4 RQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGI 63 R+P YK LY QV+ AIA+GI+LGHF+P TGVA+KPLGDGFIKLIKM+I PIIFCTVVSGI Sbjct: 3 RKPFYKILYVQVLFAIAVGIVLGHFWPATGVAMKPLGDGFIKLIKMIIGPIIFCTVVSGI 62 Query: 64 AGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYV 123 AGM++MK VG+ GG ALLYFE++ST ALLIGL+ ++++PG G +ID +TLD ++ YV Sbjct: 63 AGMRDMKKVGRVGGKALLYFEVISTFALLIGLLSAHLLKPGVGFNIDPATLDTKAISQYV 122 Query: 124 TAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRF 183 T QS V F +++IP+T+V AFANGDILQ+L+ S+ FG AL +G K V DF+++ Sbjct: 123 TQAHGQSTVEFFMHIIPDTMVSAFANGDILQILLISLFFGSALAAMGDRSKIVFDFVEQV 182 Query: 184 AHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAI 243 + V F+I+++I K+AP+GA GAMAFTIG YG+GSLV L +L+ FY T ++FV+VVLG + Sbjct: 183 SKVFFHIVHVITKVAPLGAFGAMAFTIGKYGLGSLVPLLKLIGTFYFTAIVFVVVVLGTV 242 Query: 244 CRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFN 303 R GF++ + I YI+EELLIVLGTSSSE+ALP ++ K+E LG KSVVGLV+PTGYSFN Sbjct: 243 ARLTGFNIFRFISYIKEELLIVLGTSSSEAALPHLMEKLENLGCSKSVVGLVVPTGYSFN 302 Query: 304 LDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAV 363 LDGT+IY+TMA +FIAQAT + + Q+T+L V +++SKGA+GVTGSGFI LAATL+ V Sbjct: 303 LDGTNIYMTMAVLFIAQATGIELTLLQQLTVLGVAMITSKGASGVTGSGFITLAATLAVV 362 Query: 364 GHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGRAI 423 +PVAG+ LILGIDRFMSE RALTN++GN VATVV++ W ELD QL L GG Sbjct: 363 PDIPVAGMVLILGIDRFMSECRALTNIIGNGVATVVMSAWEHELDRVQLDRMLRRGGDET 422 Query: 424 SDTRE 428 ++ E Sbjct: 423 AELAE 427 Lambda K H 0.326 0.142 0.402 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: 609 Number of extensions: 22 Number of successful extensions: 1 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: 433 Length adjustment: 32 Effective length of query: 412 Effective length of database: 401 Effective search space: 165212 Effective search space used: 165212 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 (21.6 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