Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate HSERO_RS13105 HSERO_RS13105 C4-dicarboxylate ABC transporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__HerbieS:HSERO_RS13105 Length = 441 Score = 591 bits (1524), Expect = e-173 Identities = 296/415 (71%), Positives = 350/415 (84%) Query: 2 KTSLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGI 61 K L+KSLYFQVL AI IGILLGHFYP GE MKPLGDGFVKLIKMIIAPVIFCTVV GI Sbjct: 5 KPPLYKSLYFQVLVAIVIGILLGHFYPSTGEAMKPLGDGFVKLIKMIIAPVIFCTVVIGI 64 Query: 62 AGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYA 121 AGME MK VG+TG +ALLYFE+VST+ALIIGL++VN +QPG GMNVDPA+LD K++A Y Sbjct: 65 AGMEDMKKVGKTGGLALLYFEVVSTVALIIGLLLVNFLQPGVGMNVDPASLDTKSIAAYT 124 Query: 122 DQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESF 181 K + F++ +IP S++ AFA G++LQVLL AVLFGFALH+ G +G L+F+ IE Sbjct: 125 APGKMGSVTDFVLGIIPTSMVDAFAKGDVLQVLLVAVLFGFALHKFGGRGTLVFDFIEKI 184 Query: 182 SQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSI 241 S V+F ++ IM++APIGAFGAM+FTIGKYGVG+L L +L+ FY+TC+LF+ +VLG I Sbjct: 185 SHVLFSVVGAIMKVAPIGAFGAMSFTIGKYGVGSLFSLAKLMGTFYLTCLLFIFVVLGII 244 Query: 242 AKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFN 301 + GFSI+KF++YI+EELLIVLGTSSSES LPRML KME G +K+VVGLVIPTGYSFN Sbjct: 245 TRLHGFSIWKFVKYIKEELLIVLGTSSSESVLPRMLAKMENAGAKKTVVGLVIPTGYSFN 304 Query: 302 LDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAV 361 LDGT+IYLTMAAVFIAQATN+ M V ++TLL VLLL+SKGAAG+TGSGFIVLAATLSAV Sbjct: 305 LDGTAIYLTMAAVFIAQATNTPMTFVQELTLLGVLLLTSKGAAGITGSGFIVLAATLSAV 364 Query: 362 GHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNN 416 GH+PVAGLALILGIDRFMSEARALTN +GNGVAT+VVAKW ELD ++L VLNN Sbjct: 365 GHVPVAGLALILGIDRFMSEARALTNTIGNGVATLVVAKWSGELDSERLTKVLNN 419 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: 650 Number of extensions: 28 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: 428 Length of database: 441 Length adjustment: 32 Effective length of query: 396 Effective length of database: 409 Effective search space: 161964 Effective search space used: 161964 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