Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate H281DRAFT_03740 H281DRAFT_03740 Crotonobetainyl-CoA:carnitine CoA-transferase CaiB
Query= SwissProt::Q9HAC7 (445 letters) >FitnessBrowser__Burk376:H281DRAFT_03740 Length = 388 Score = 278 bits (710), Expect = 3e-79 Identities = 143/377 (37%), Positives = 228/377 (60%), Gaps = 2/377 (0%) Query: 47 PLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTR-TWGPPFVGTESTYYLS 105 PL+G+++LD+++V+AGPFA M L DLGA+VIKVE P GD TR + G G +S +L+ Sbjct: 8 PLQGIRVLDVSQVMAGPFACMMLADLGADVIKVE-PPEGDQTRGSMGFKMKGPDSMGFLN 66 Query: 106 VNRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIYC 165 +NRNK+S+ +++K +G ++ +LA DV VENY PG + + + YE I I P I+Y Sbjct: 67 LNRNKRSVTLDLKSDEGRELFYKLAKTADVIVENYRPGVVQRLRIDYESIKAINPKIVYA 126 Query: 166 SITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDPVRPGVAMTDLATGLYAYGAIMA 225 SI+G+GQ+GP + R G+D +A A+SG+M +TG + G PV+ GV + D+ ++A +++ Sbjct: 127 SISGFGQSGPWASRPGFDLMAQAMSGVMSVTGYKGGKPVKAGVPVADIGCAMFAVYGLLS 186 Query: 226 GLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLIGQKEAKRWGTAHGSIVPYQAFKTKD 285 I KTG+G ID +L S +A ++Y GT++ PYQA K +D Sbjct: 187 AYIGAQKTGEGQHIDASLFDSIMAFSIWDMSDYWGTGVPPTPLGTSNKMSAPYQAVKARD 246 Query: 286 GYIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKILSERFEEELTSKW 345 GY V+GA N + + +C +L+ P+LID++ Y LR+ NR+ +I++L + F + +++W Sbjct: 247 GYFVMGATNQKLWTKLCHVLERPDLIDHADYANVSLRLKNREAMIEVLEQEFGKRDSNEW 306 Query: 346 LYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVRYSKFKMSEA 405 + + +G+P GPI + F H + ME++HP GK+ G V+ + Sbjct: 307 VDILLAAGIPAGPILSYPEAFESDHARHRNMCMEIDHPNEGKVKNIGFPVKLLGTPPTVR 366 Query: 406 RPPPLLGQHTTHILKEV 422 R PPLLG+H I E+ Sbjct: 367 RHPPLLGEHNEEIFAEI 383 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: 445 Number of extensions: 23 Number of successful extensions: 2 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: 388 Length adjustment: 31 Effective length of query: 414 Effective length of database: 357 Effective search space: 147798 Effective search space used: 147798 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