Align Acyl-CoA synthetase short-chain family member 3, mitochondrial; Acetate--CoA ligase 3; Acyl-CoA synthetase short-chain family member 3; Propionate--CoA ligase; EC 6.2.1.1; EC 6.2.1.17 (characterized)
to candidate H281DRAFT_05523 H281DRAFT_05523 propionyl-CoA synthetase (EC 6.2.1.17)
Query= SwissProt::Q9H6R3 (686 letters) >FitnessBrowser__Burk376:H281DRAFT_05523 Length = 648 Score = 613 bits (1581), Expect = e-180 Identities = 309/625 (49%), Positives = 417/625 (66%), Gaps = 16/625 (2%) Query: 71 TDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHIENGKGDKIA 130 TDP FW +AA ++W +PW + L ++ WF N YN +DRH+E G+G+++A Sbjct: 12 TDPMAFWARAASSVAWSRPWDEVLTHQPGQRFSWFDGAYTNASYNCLDRHVEAGRGEQVA 71 Query: 131 IIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQAMYTMLACAR 190 I ++SPVT T T TY + +QV+ AGVL G++ GD VVIYMP+IPQA+ MLACAR Sbjct: 72 IAFESPVTGTAQTLTYASLRDQVAGFAGVLQLQGVRMGDVVVIYMPVIPQAIIAMLACAR 131 Query: 191 IGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEALKIGQHKPD 250 IGA H ++FGGFA+ EL+ R+ P+V+VTAS G E RR+ Y V+EA+ + Sbjct: 132 IGATHCVVFGGFAASELAKRLRDTLPRVIVTASCGFEVKRRIPYKETVDEAV-LQSAWQG 190 Query: 251 KILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLPKGVI 310 +++Y R + V LA RD+DW+ M +PV + HPLYIL+TSGTTG PKG+ Sbjct: 191 PVIVYQR-ELGRVELAE-RDVDWERAMCGTYGVSPIPVPAGHPLYILHTSGTTGSPKGIQ 248 Query: 311 RPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYEGKPV 370 R TGGY L WSM++IY PG+V+WAASD+GWVVGHSY+ YGPLL+G TTVL+EGKPV Sbjct: 249 RDTGGYMTALLWSMNNIYRSLPGDVFWAASDIGWVVGHSYMTYGPLLNGCTTVLFEGKPV 308 Query: 371 GTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGA---------ALGKQYSLTRFKTL 421 GTPDA A++RV+A+H V LFTAPTA+RAI+++DPG L +Y L +++ Sbjct: 309 GTPDAAAFWRVIAKHRVNVLFTAPTALRAIKKEDPGGYQLREPVMGELHWRYDLGSLRSV 368 Query: 422 FVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCV--GLGNSKTPPPGQAGKSV 479 F+AGERCD T+EW++++ VPVLDHWWQTE G P+ AS LG + G AG+++ Sbjct: 369 FLAGERCDTTTIEWAEDLLHVPVLDHWWQTEAGWPMAASTAKGALGGERRR--GAAGRAL 426 Query: 480 PGYNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMD 539 PG++V +DD ++ A GN+V LPLPPGA + +W E ++ YF +FPG+YDT D Sbjct: 427 PGWDVRCVDDQGAEVDAGASGNVVCGLPLPPGAMTTIWNAHERYERSYFGRFPGWYDTGD 486 Query: 540 AGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHVPL 599 AGY+D +G+++VM R DDVINVAGHR+S GAIEE + VA+CAVVG PLKG VPL Sbjct: 487 AGYVDADGFVFVMGRTDDVINVAGHRLSTGAIEEIVSRLDAVAECAVVGMAHPLKGQVPL 546 Query: 600 ALCVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSAIV 659 VL+ + VK VR+ +G VA+ + A V++LPKTRSGKI R +L IV Sbjct: 547 VFLVLKDGSKDGADAAETAAVKVVREQLGAVASMQAAFVVERLPKTRSGKILRRSLLQIV 606 Query: 660 NGKPYKITSTIEDPSIFGHVEEMLK 684 +GK I +TIEDP + VE ++K Sbjct: 607 DGKAVAIPATIEDPGVLVDVERIVK 631 Lambda K H 0.318 0.136 0.422 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: 1260 Number of extensions: 61 Number of successful extensions: 4 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: 686 Length of database: 648 Length adjustment: 38 Effective length of query: 648 Effective length of database: 610 Effective search space: 395280 Effective search space used: 395280 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: 54 (25.4 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