Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate Pf1N1B4_4464 C4-dicarboxylate transport protein
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4464 Length = 439 Score = 455 bits (1171), Expect = e-132 Identities = 218/393 (55%), Positives = 304/393 (77%) Query: 9 KSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQN 68 KSLYFQ++ A+ +G+++GHF+ Q +ALKPLGD FIKLIKM+IAP++FCT+V+GIAGM + Sbjct: 9 KSLYFQILCAVLLGVVVGHFWAQQAIALKPLGDAFIKLIKMMIAPVVFCTIVTGIAGMND 68 Query: 69 MKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAGKD 128 +S+G+ +L F ++ I+L IGLV V V +PG GM+ID S L + ++ Y + Sbjct: 69 KRSLGRLLSKTMLLFLGLTVISLFIGLVAVYVFKPGAGMNIDPSHLSTAGLSQYTESAAK 128 Query: 129 QSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHVMF 188 +V F +++IP+T +GAF+ G++L VL +V+ GFAL LG GKPVLD ++ + ++F Sbjct: 129 LGVVEFFMHIIPDTFIGAFSKGEVLPVLFIAVLCGFALSSLGDRGKPVLDVLEAASQMVF 188 Query: 189 NIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRAHG 248 I + +M+ APIGA GA+AFT+G YG+ SL L +L++ Y+ C FV VVLG+ICRAHG Sbjct: 189 KIFSYLMRFAPIGAFGALAFTVGQYGITSLGSLAKLIMTLYVACAFFVFVVLGSICRAHG 248 Query: 249 FSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDGTS 308 FS+ KL+RY+REE L+VLGTSS+E +PRML K++ LG K VVGLV+PTGYSFNLDGT+ Sbjct: 249 FSLWKLLRYLREEFLVVLGTSSTEPVMPRMLEKLQALGCSKGVVGLVLPTGYSFNLDGTA 308 Query: 309 IYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPV 368 IYL++AA+FIAQA + + +T +T+L ++LLSSKGAAGVTGSGF+ LA+TL+ + +P+ Sbjct: 309 IYLSLAAIFIAQACNIDLTVTQTLTMLAIMLLSSKGAAGVTGSGFVALASTLTVIHDIPL 368 Query: 369 AGLALILGIDRFMSEARALTNLVGNAVATVVVA 401 AGLAL++GIDRFMSEARALT+L NAVATVV++ Sbjct: 369 AGLALLIGIDRFMSEARALTSLASNAVATVVIS 401 Lambda K H 0.326 0.142 0.402 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: 549 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: 444 Length of database: 439 Length adjustment: 32 Effective length of query: 412 Effective length of database: 407 Effective search space: 167684 Effective search space used: 167684 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 (21.6 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