Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate HSERO_RS22690 HSERO_RS22690 C4-dicarboxylate ABC transporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__HerbieS:HSERO_RS22690 Length = 444 Score = 442 bits (1138), Expect = e-129 Identities = 219/419 (52%), Positives = 306/419 (73%), Gaps = 3/419 (0%) Query: 3 TSLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIA 62 + LFKSL+ QV+ A+ GI++G F+P+ G+ +KPLGDGF+KLIKMII ++FC VV GI Sbjct: 2 SKLFKSLFGQVVLALIGGIIIGLFWPDFGQNLKPLGDGFIKLIKMIIPVIVFCVVVQGIC 61 Query: 63 GMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVY-- 120 G +K VG G A++YFE+V+TIAL++GL++ VVQPGAGMN+DP+ LDA +++ Y Sbjct: 62 GASDLKKVGSVGVKAIIYFEVVTTIALLLGLVLALVVQPGAGMNIDPSNLDASSLSGYMA 121 Query: 121 -ADQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIE 179 A + K+ G FIM +IPA+ + AF SG++LQVLL +V FG AL +G KG + ++ Sbjct: 122 NAGKVKETGFAEFIMKLIPATAVSAFTSGDVLQVLLISVTFGCALLLIGEKGAPVVALVA 181 Query: 180 SFSQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLG 239 S S F ++ +RLAP+G GA+AFT+GKYG+G+L QL L++ FY I FV++VLG Sbjct: 182 SLSDAFFKCMSFFIRLAPLGVLGAIAFTVGKYGIGSLKQLALLVLLFYGAVIFFVLVVLG 241 Query: 240 SIAKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYS 299 I +A+G SIFK IRY+REEL++VL T+SS+S LP+++ K+E +G +KS VGLVIPTGYS Sbjct: 242 GILRASGLSIFKLIRYLREELVVVLATTSSDSVLPQIMKKLEHMGIKKSTVGLVIPTGYS 301 Query: 300 FNLDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLS 359 FNLD SIYLTMAA+FIAQATN+ + + +L + L++SKGA GV GS ++LAATL+ Sbjct: 302 FNLDAFSIYLTMAALFIAQATNTHLSMGDLAAILAIALVTSKGAHGVPGSAIVILAATLT 361 Query: 360 AVGHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRA 418 + +PV GL L+L ID F+ ARAL NL+GN VAT+V+A W +++D + VLN + Sbjct: 362 TIPAIPVVGLVLVLSIDWFIGIARALGNLLGNCVATVVIASWERDIDKVRARAVLNGES 420 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: 581 Number of extensions: 37 Number of successful extensions: 5 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: 444 Length adjustment: 32 Effective length of query: 396 Effective length of database: 412 Effective search space: 163152 Effective search space used: 163152 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