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 GFF2099 HP15_2053 PrpE protein
Query= SwissProt::Q9H6R3 (686 letters) >FitnessBrowser__Marino:GFF2099 Length = 624 Score = 636 bits (1641), Expect = 0.0 Identities = 313/629 (49%), Positives = 425/629 (67%), Gaps = 10/629 (1%) Query: 61 EYKTHFAASVTDPERFWGKAAEQISWYKP----WTKTLENKHSPSTRWFVEGMLNICYNA 116 +Y + F S+ P+ FW + AE+I W +P W T +N H +WF +G LN C A Sbjct: 2 DYHSEFRRSIDKPDEFWREQAEKIDWIEPPKTIWQPT-DNGHG---QWFPDGTLNTCDVA 57 Query: 117 VDRHIENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMP 176 +D +I G+GD+ A+IYDSPVT+T+ ++TY E+ ++V++ AG L GI KGD V+IYMP Sbjct: 58 LDANIRAGRGDQKALIYDSPVTDTQRSYTYNELTDEVARFAGALKDRGITKGDRVIIYMP 117 Query: 177 MIPQAMYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVP 236 MIP+A+ ML CARIGAIHS++FGGFA+ EL+ RID KPK V+TAS GIE R +EY P Sbjct: 118 MIPEAVIAMLGCARIGAIHSVVFGGFAAHELAVRIDDAKPKAVITASCGIEVTRVIEYKP 177 Query: 237 LVEEALKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYI 296 LV++A+ HKP+ ++Y R ++A L RD DW+E M A+ D VPV S PLYI Sbjct: 178 LVDKAIDQASHKPETCIVYQRQQVQA-ELQACRDHDWNELMETAEPADPVPVKSTDPLYI 236 Query: 297 LYTSGTTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPL 356 LYTSGTTG PKGV+R GG+AV L++SM +Y +PG+V+WAASD+GWVVGHSYI Y PL Sbjct: 237 LYTSGTTGKPKGVVRDNGGHAVALNYSMKLVYDAKPGDVYWAASDVGWVVGHSYIVYAPL 296 Query: 357 LHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLT 416 G TT++YEGKPV TPDAGA++RV+ +H V LFTAPTA RA+R++DP A +Y ++ Sbjct: 297 FAGCTTIMYEGKPVKTPDAGAFWRVVQDHKVNMLFTAPTAFRAVRKEDPEADQLSRYDIS 356 Query: 417 RFKTLFVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAG 476 K LF+AGER D T EW K +PVLDHWWQTETG I + VG+ T PG A Sbjct: 357 SLKRLFLAGERLDPATYEWLKEHTGLPVLDHWWQTETGWAICCNPVGIELMAT-KPGSAT 415 Query: 477 KSVPGYNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYD 536 PGYNV ++D N ++ A G I VKLPLPPG +W + E F+ Y E G+Y Sbjct: 416 VPSPGYNVQVVDMNGSQMPAGEQGQIAVKLPLPPGCMMTVWGDDERFRKTYLEPISGFYS 475 Query: 537 TMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGH 596 + D G++D++GY++VM R DDVINVAGHR+S G +EE + SH +A+C VVG D +KG Sbjct: 476 SGDGGFIDDDGYVFVMGRTDDVINVAGHRLSTGEMEEVVASHPAIAECCVVGAHDDMKGQ 535 Query: 597 VPLALCVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALS 656 +P+ L +++ +++ +E+V+ VR IG +A FR A+ V +LPKTRSGKI R + Sbjct: 536 IPIGLVLIKDGATIDHDELEDELVEMVRDKIGAIACFRRALVVDRLPKTRSGKILRRVIR 595 Query: 657 AIVNGKPYKITSTIEDPSIFGHVEEMLKQ 685 I +G+ Y + STI+DP+I + E ++ Sbjct: 596 QIADGEEYSVPSTIDDPAILEEISEQFRR 624 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: 1175 Number of extensions: 44 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: 686 Length of database: 624 Length adjustment: 38 Effective length of query: 648 Effective length of database: 586 Effective search space: 379728 Effective search space used: 379728 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