Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate Pf1N1B4_4464 C4-dicarboxylate transport protein
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4464 Length = 439 Score = 463 bits (1191), Expect = e-135 Identities = 223/413 (53%), Positives = 312/413 (75%) Query: 7 KSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMES 66 KSLYFQ+L A+ +G+++GHF+ + +KPLGD F+KLIKM+IAPV+FCT+VTGIAGM Sbjct: 9 KSLYFQILCAVLLGVVVGHFWAQQAIALKPLGDAFIKLIKMMIAPVVFCTIVTGIAGMND 68 Query: 67 MKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKD 126 +++GR + +L F ++ I+L IGL+ V V +PGAGMN+DP+ L ++ Y + A Sbjct: 69 KRSLGRLLSKTMLLFLGLTVISLFIGLVAVYVFKPGAGMNIDPSHLSTAGLSQYTESAAK 128 Query: 127 QGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVIF 186 G+V F M +IP + IGAF+ G +L VL AVL GFAL LG +G+ + +V+E+ SQ++F Sbjct: 129 LGVVEFFMHIIPDTFIGAFSKGEVLPVLFIAVLCGFALSSLGDRGKPVLDVLEAASQMVF 188 Query: 187 GIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKATG 246 I + +MR APIGAFGA+AFT+G+YG+ +L L +LI+ Y+ C FV +VLGSI +A G Sbjct: 189 KIFSYLMRFAPIGAFGALAFTVGQYGITSLGSLAKLIMTLYVACAFFVFVVLGSICRAHG 248 Query: 247 FSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGTS 306 FS++K +RY+REE L+VLGTSS+E +PRML+K++ LGC K VVGLV+PTGYSFNLDGT+ Sbjct: 249 FSLWKLLRYLREEFLVVLGTSSTEPVMPRMLEKLQALGCSKGVVGLVLPTGYSFNLDGTA 308 Query: 307 IYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPV 366 IYL++AA+FIAQA N + + +T+L ++LLSSKGAAGVTGSGF+ LA+TL+ + +P+ Sbjct: 309 IYLSLAAIFIAQACNIDLTVTQTLTMLAIMLLSSKGAAGVTGSGFVALASTLTVIHDIPL 368 Query: 367 AGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAP 419 AGLAL++GIDRFMSEARALT+L N VAT+V++ D + L D L+ + P Sbjct: 369 AGLALLIGIDRFMSEARALTSLASNAVATVVISISENACDRQVLLDTLDGKKP 421 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: 532 Number of extensions: 20 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: 439 Length adjustment: 32 Effective length of query: 396 Effective length of database: 407 Effective search space: 161172 Effective search space used: 161172 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