Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate Pf1N1B4_3488 Alpha-methylacyl-CoA racemase (EC 5.1.99.4)
Query= SwissProt::Q9HAC7 (445 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3488 Length = 393 Score = 172 bits (436), Expect = 2e-47 Identities = 125/403 (31%), Positives = 202/403 (50%), Gaps = 24/403 (5%) Query: 47 PLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTESTYYLSV 106 PL +K+LD + +L GPFA++ L D+GAEV+++E P D R P G +++ + Sbjct: 4 PLASLKVLDFSTLLPGPFASLLLADMGAEVLRIESPTRMDLLRVLPPHDQGVSASHAY-L 62 Query: 107 NRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIYCS 166 NRNK+S+A+++K P+ +++IK+L D+ +E + PG + +GLGYE + I P +IY S Sbjct: 63 NRNKRSLALDLKQPEALEVIKQLLQDHDIVLEQFRPGVMDRLGLGYEALKAINPKLIYVS 122 Query: 167 ITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDPVRPGVAMTDLATG-LYAYGAIMA 225 ITGYGQTGP RAG+D A++GL TG + PV G+ + D+A G L+ ++A Sbjct: 123 ITGYGQTGPYKDRAGHDINYLALAGLSSYTGRADSGPVPLGMQVADVAGGSLHGVIGLLA 182 Query: 226 GLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLIGQKEAKRWGTAHGSIVPYQAFKTKD 285 +I + +TG+G +D ++ + + A YL E R Y ++++D Sbjct: 183 AVIARQQTGQGQHLDVSMTDCAFSLNAMAGAGYLACGVEPGREEQMLNGGSFYDYYRSRD 242 Query: 286 G-YIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKILSERFEEELTSK 344 G ++ VG+ +C L PEL R KE +KI E+++ ++ Sbjct: 243 GRWLSVGSLEPVFMQQLCMALGRPELAAQG-LSPQPARQQALKEALKIEFEKYD---FAQ 298 Query: 345 WLYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEM---EHPTVGKISVPGPAVRYSKFK 401 LF G P+ ++ PQ+ LV E+ + T +++ P K Sbjct: 299 LCELFAGVDACVEPVLSLGEAVRHPQLKARELVTEVPRGDGSTQAQMACP--------LK 350 Query: 402 MSEARPPPL-----LGQHTTHILKEVLRYDDRAIGELLSAGVV 439 S P P LG+HT +L L + I EL A V+ Sbjct: 351 FSAGLPEPRHIGAGLGEHTDQVL-GALGFSVERIEELRRARVI 392 Lambda K H 0.318 0.137 0.410 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: 456 Number of extensions: 26 Number of successful extensions: 3 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: 445 Length of database: 393 Length adjustment: 32 Effective length of query: 413 Effective length of database: 361 Effective search space: 149093 Effective search space used: 149093 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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