Align C4-dicarboxylate transport protein 2 (characterized)
to candidate RR42_RS26105 RR42_RS26105 C4-dicarboxylate transporter
Query= SwissProt::Q9I4F5 (436 letters) >FitnessBrowser__Cup4G11:RR42_RS26105 Length = 462 Score = 615 bits (1587), Expect = 0.0 Identities = 306/420 (72%), Positives = 355/420 (84%) Query: 4 QPFYKSLYVQVLVAIAIGIALGHWYPETAVAMKPFGDGFVKLIKMAIAPIIFCTVVTGIA 63 +PFY+SLY QV+ AI IG+ LGH+YP+ AMKP GDGF+KLIKM IAPIIFCTVV GIA Sbjct: 20 KPFYRSLYFQVITAIVIGVILGHFYPQAGAAMKPLGDGFIKLIKMIIAPIIFCTVVVGIA 79 Query: 64 GMQSMKSVGKTGGMALLYFEVVSTVALIIGLVVVNVVQPGAGMHVDPNTLDTSKIAAYAA 123 GM+ MK VGKTGG+ALLYFEVVS +AL++GLV++N+ +PG GM+VD +TLDT IAAY Sbjct: 80 GMEDMKKVGKTGGLALLYFEVVSAIALVVGLVIINIAKPGVGMNVDVSTLDTKSIAAYTG 139 Query: 124 AGEKQSTVDFLMNVIPGTVVGAFANGDILQVLFFSVLFGYALHRLGSYGKPVFEFIERVS 183 G+ Q TVDFL++VIP TVV AFA G+ILQVL F+V+FG+ALH+ G G VF+FIE+ S Sbjct: 140 PGKMQGTVDFLLHVIPNTVVDAFAQGEILQVLLFAVMFGFALHKFGGRGTLVFDFIEKFS 199 Query: 184 HVMFNIINVIMKVAPIGAFGAMAFTIGAYGVGSLVQLGQLMLCFYITCILFVLIVLGGIA 243 HV+F I+ IMKVAPIGAFGAMAFTIG YGVGSL+QLGQLM FY TC+ F+ +VLGGIA Sbjct: 200 HVLFAIVGYIMKVAPIGAFGAMAFTIGKYGVGSLLQLGQLMATFYATCLFFIFVVLGGIA 259 Query: 244 RAHGFSILRFIRYIREELLIVLGTSSSESALPRMIDKMEKLGCNKSVVGLVIPTGYSFNL 303 RAHGFSI +FI+YI+EELLIVLGTSSSES LPRM+ K+E LG KSVVGLVIPTGYSFNL Sbjct: 260 RAHGFSIWKFIKYIKEELLIVLGTSSSESVLPRMMAKLENLGARKSVVGLVIPTGYSFNL 319 Query: 304 DGTSIYLTMAAVFIAQATDTPMDITHQITLLLVLLIASKGAAGVTGSGFIVLAATLSAVG 363 DGTSIYLTMAAVFIAQAT+T M +T Q+TLL VLL+ SKGAAGVTGSGFIVLAATLSAVG Sbjct: 320 DGTSIYLTMAAVFIAQATNTEMSLTQQLTLLAVLLLTSKGAAGVTGSGFIVLAATLSAVG 379 Query: 364 HLPVAGLALILGIDRFMSEARALTNLVGNGVATVVVSKWCKQLDEGTLQRELAGEGNASS 423 H+PVAGLALILGIDRFMSEARALTNL+GNGVATVVV+KW LD + R L E +A + Sbjct: 380 HVPVAGLALILGIDRFMSEARALTNLIGNGVATVVVAKWTGDLDVARMHRRLDNESDAEA 439 Lambda K H 0.325 0.140 0.406 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: 705 Number of extensions: 24 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: 436 Length of database: 462 Length adjustment: 33 Effective length of query: 403 Effective length of database: 429 Effective search space: 172887 Effective search space used: 172887 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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