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 WP_043768476.1 U743_RS11510 propionyl-CoA synthetase
Query= SwissProt::Q9H6R3 (686 letters) >NCBI__GCF_000733765.1:WP_043768476.1 Length = 630 Score = 683 bits (1762), Expect = 0.0 Identities = 318/627 (50%), Positives = 442/627 (70%), Gaps = 3/627 (0%) Query: 58 SGSEYKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPST-RWFVEGMLNICYNA 116 + Y+T + S+ +PE FW + AE + W + W + L + + RWF G LN CYNA Sbjct: 2 AAGRYETEYRQSIDNPESFWAEQAEALHWERRWDRVLSHDDADGAPRWFAGGRLNTCYNA 61 Query: 117 VDRHIENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMP 176 VDRH++ G+G++IA+I+DSPVT++ F++ E+ + ++LAG L G++ GD VVIYMP Sbjct: 62 VDRHVDAGRGEQIALIHDSPVTDSVRRFSFIELRDATARLAGALRAAGVETGDRVVIYMP 121 Query: 177 MIPQAMYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVP 236 MI +A MLACARIGA+HS++FGGFA+ EL+ RID KPK +++AS GIE R + Y P Sbjct: 122 MIAEAAIAMLACARIGAVHSVVFGGFAAPELAKRIDDAKPKAILSASCGIEGSRVIAYKP 181 Query: 237 LVEEALKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYI 296 LV+ A++ HKP LI RP EA L+ GRD DW++ +A A DCVPV + PLY+ Sbjct: 182 LVDAAIEAASHKPQSCLILQRPQCEA-ELSAGRDRDWEQAVAAAGPADCVPVEATDPLYV 240 Query: 297 LYTSGTTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPL 356 LYTSGTTG PKGV+R GG+AV L +SM ++Y + PGEV+WAASD+GWVVGHSYI Y PL Sbjct: 241 LYTSGTTGKPKGVVRDNGGHAVALTYSMKAVYDMNPGEVFWAASDVGWVVGHSYIVYAPL 300 Query: 357 LHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLT 416 L G TTV++EGKPVGTPDAGA++RV +EHGV ALFTAPTA RAI+++DP +Y L Sbjct: 301 LAGCTTVMFEGKPVGTPDAGAFWRVASEHGVKALFTAPTAFRAIKKEDPKGEHLARYKLA 360 Query: 417 RFKTLFVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAG 476 F+ L++AGERCD +T++W+ + +VPV+DHWWQTETG P+ A C GL + P G AG Sbjct: 361 AFEALYLAGERCDPDTIDWASGLLQVPVIDHWWQTETGWPVAAVCRGL-QDEAPHIGSAG 419 Query: 477 KSVPGYNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYD 536 + VPGY++ +LDD+ ++ +GNIV++ PLPPG LW N++ F+ Y ++PG+Y Sbjct: 420 RPVPGYDIRVLDDDGHEVPRDAIGNIVIRQPLPPGTLPTLWNNEQGFRENYLARYPGHYL 479 Query: 537 TMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGH 596 T DAG +D EGY++VMSR+DD+INVAGHR+S GA+EE + H VA+CAV+ D KG Sbjct: 480 TGDAGKIDAEGYVWVMSRIDDIINVAGHRLSTGAMEEVLAGHPDVAECAVIAVADATKGQ 539 Query: 597 VPLALCVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALS 656 +P+ + VL+ ++ E + E+++ VR IG VAAF+ A+ V +LPKTRSGK+ R + Sbjct: 540 LPVGMVVLKSGVDRDTEVITRELIQRVRDEIGAVAAFKRAIVVPRLPKTRSGKVLRKTMR 599 Query: 657 AIVNGKPYKITSTIEDPSIFGHVEEML 683 +I NG+ + +TI+DP+I + E L Sbjct: 600 SIANGENLTVPATIDDPAILDEIREAL 626 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: 1210 Number of extensions: 70 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: 630 Length adjustment: 38 Effective length of query: 648 Effective length of database: 592 Effective search space: 383616 Effective search space used: 383616 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 24 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