Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate RR42_RS26105 RR42_RS26105 C4-dicarboxylate transporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Cup4G11:RR42_RS26105 Length = 462 Score = 613 bits (1580), Expect = e-180 Identities = 307/424 (72%), Positives = 359/424 (84%) Query: 5 QPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIA 64 +P Y+SLYFQVI AI IG++LGHFYPQ G A+KPLGDGFIKLIKM+IAPIIFCTVV GIA Sbjct: 20 KPFYRSLYFQVITAIVIGVILGHFYPQAGAAMKPLGDGFIKLIKMIIAPIIFCTVVVGIA 79 Query: 65 GMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVT 124 GM++MK VGKTGG ALLYFE+VS IAL++GLV++N+ +PG GM++DVSTLD +AAY Sbjct: 80 GMEDMKKVGKTGGLALLYFEVVSAIALVVGLVIINIAKPGVGMNVDVSTLDTKSIAAYTG 139 Query: 125 AGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFA 184 GK Q V F+L+VIPNT+V AFA G+ILQVL+F+V+FGFALH+ G G V DFI++F+ Sbjct: 140 PGKMQGTVDFLLHVIPNTVVDAFAQGEILQVLLFAVMFGFALHKFGGRGTLVFDFIEKFS 199 Query: 185 HVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAIC 244 HV+F I+ IMK+APIGA GAMAFTIG YGVGSL+QLGQLM FY TC+ F+ VVLG I Sbjct: 200 HVLFAIVGYIMKVAPIGAFGAMAFTIGKYGVGSLLQLGQLMATFYATCLFFIFVVLGGIA 259 Query: 245 RAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNL 304 RAHGFS+ K I+YI+EELLIVLGTSSSES LPRM+ K+E LGA+KSVVGLVIPTGYSFNL Sbjct: 260 RAHGFSIWKFIKYIKEELLIVLGTSSSESVLPRMMAKLENLGARKSVVGLVIPTGYSFNL 319 Query: 305 DGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVG 364 DGTSIYLTMAAVFIAQAT+T M +T Q+TLL VLLL+SKGAAGVTGSGFIVLAATLSAVG Sbjct: 320 DGTSIYLTMAAVFIAQATNTEMSLTQQLTLLAVLLLTSKGAAGVTGSGFIVLAATLSAVG 379 Query: 365 HLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGRAIS 424 H+PVAGLALILGIDRFMSEARALTNL+GN VATVVVAKW +LD ++ L + A + Sbjct: 380 HVPVAGLALILGIDRFMSEARALTNLIGNGVATVVVAKWTGDLDVARMHRRLDNESDAEA 439 Query: 425 DTRE 428 D E Sbjct: 440 DEPE 443 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: 685 Number of extensions: 26 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: 462 Length adjustment: 33 Effective length of query: 411 Effective length of database: 429 Effective search space: 176319 Effective search space used: 176319 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