Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate H281DRAFT_03336 H281DRAFT_03336 Na+/H+-dicarboxylate symporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Burk376:H281DRAFT_03336 Length = 438 Score = 445 bits (1144), Expect = e-129 Identities = 216/423 (51%), Positives = 303/423 (71%) Query: 9 KSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQN 68 +SLY QV++ + +G+ +GHF PQ G LKP D F+ L++M+IAPI+FCT+VSGI + + Sbjct: 8 RSLYVQVLLGMVLGVAVGHFLPQAGALLKPFSDAFVGLVRMMIAPIVFCTIVSGITSLAS 67 Query: 69 MKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAGKD 128 K++G+T AL F +++ +AL GLV V++PG GMHID LD S +A YV + Sbjct: 68 GKAIGRTIFKALALFYLLTVVALAFGLVTAIVLRPGAGMHIDAHGLDTSILAQYVKHAQP 127 Query: 129 QSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHVMF 188 +V F L+VIP T++GAF GD+L VL+ S++FGF+L+ G+PVL ID AHV+F Sbjct: 128 GGLVAFALSVIPETMLGAFEKGDVLPVLLLSLLFGFSLNSCPKAGRPVLALIDGVAHVLF 187 Query: 189 NIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRAHG 248 I+ MIM+LAP+GA GAMAFT+G +G+ S+ LG LM+CFY+ C+LF+ +VL ++ R HG Sbjct: 188 RILAMIMRLAPLGAFGAMAFTVGRFGIRSVGSLGMLMVCFYVACLLFIALVLASLARLHG 247 Query: 249 FSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDGTS 308 F++ +L+RY+REELLIVL TSS+E LPR+++K+E LG K VVGLV+P GYSFNLDGT+ Sbjct: 248 FALWRLLRYMREELLIVLATSSTEPVLPRLIVKLEALGCDKGVVGLVLPAGYSFNLDGTA 307 Query: 309 IYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPV 368 IYLT+A++FIAQA D + + +L V+LL+SKGAAGV+GSG + L ATL+ + LPV Sbjct: 308 IYLTLASMFIAQACDVPLSASQIAMMLAVMLLTSKGAAGVSGSGLVALVATLTVIPDLPV 367 Query: 369 AGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGRAISDTRE 428 AG+AL++GIDRFMSEARALT+++ NA A + V+ W D +L L + D Sbjct: 368 AGVALLVGIDRFMSEARALTSVISNACAVIFVSMWEGACDRARLAQMLGAAAAPAGDADG 427 Query: 429 EDD 431 +D Sbjct: 428 AED 430 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: 553 Number of extensions: 29 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: 438 Length adjustment: 32 Effective length of query: 412 Effective length of database: 406 Effective search space: 167272 Effective search space used: 167272 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