Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate RR42_RS26105 RR42_RS26105 C4-dicarboxylate transporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__Cup4G11:RR42_RS26105 Length = 462 Score = 603 bits (1555), Expect = e-177 Identities = 298/411 (72%), Positives = 355/411 (86%), Gaps = 4/411 (0%) Query: 6 FKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGME 65 ++SLYFQV+TAI IG++LGHFYP+ G MKPLGDGF+KLIKMIIAP+IFCTVV GIAGME Sbjct: 23 YRSLYFQVITAIVIGVILGHFYPQAGAAMKPLGDGFIKLIKMIIAPIIFCTVVVGIAGME 82 Query: 66 SMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAK 125 MK VG+TG +ALLYFE+VS IAL++GL+I+N+ +PG GMNVD +TLD K++A Y K Sbjct: 83 DMKKVGKTGGLALLYFEVVSAIALVVGLVIINIAKPGVGMNVDVSTLDTKSIAAYTGPGK 142 Query: 126 DQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVI 185 QG V F++ VIP +V+ AFA G ILQVLLFAV+FGFALH+ G +G L+F+ IE FS V+ Sbjct: 143 MQGTVDFLLHVIPNTVVDAFAQGEILQVLLFAVMFGFALHKFGGRGTLVFDFIEKFSHVL 202 Query: 186 FGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKAT 245 F I+ IM++APIGAFGAMAFTIGKYGVG+L+QLGQL+ FY TC+ F+ +VLG IA+A Sbjct: 203 FAIVGYIMKVAPIGAFGAMAFTIGKYGVGSLLQLGQLMATFYATCLFFIFVVLGGIARAH 262 Query: 246 GFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT 305 GFSI+KFI+YI+EELLIVLGTSSSES LPRM+ K+E LG RKSVVGLVIPTGYSFNLDGT Sbjct: 263 GFSIWKFIKYIKEELLIVLGTSSSESVLPRMMAKLENLGARKSVVGLVIPTGYSFNLDGT 322 Query: 306 SIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP 365 SIYLTMAAVFIAQATN++M + Q+TLL VLLL+SKGAAGVTGSGFIVLAATLSAVGH+P Sbjct: 323 SIYLTMAAVFIAQATNTEMSLTQQLTLLAVLLLTSKGAAGVTGSGFIVLAATLSAVGHVP 382 Query: 366 VAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELD----HKKLDD 412 VAGLALILGIDRFMSEARALTNL+GNGVAT+VVAKW +LD H++LD+ Sbjct: 383 VAGLALILGIDRFMSEARALTNLIGNGVATVVVAKWTGDLDVARMHRRLDN 433 Lambda K H 0.327 0.142 0.401 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: 632 Number of extensions: 20 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 428 Length of database: 462 Length adjustment: 32 Effective length of query: 396 Effective length of database: 430 Effective search space: 170280 Effective search space used: 170280 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: 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