Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate GFF1175 PGA1_c11900 propionate-CoA ligase PrpE
Query= BRENDA::A0A0G2K047 (683 letters) >FitnessBrowser__Phaeo:GFF1175 Length = 629 Score = 674 bits (1738), Expect = 0.0 Identities = 321/614 (52%), Positives = 426/614 (69%), Gaps = 2/614 (0%) Query: 67 ADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHIENGQGDKIA 126 A+PE+FW +AAE ISW TK L ++ WF + +N CYNA+DRH+E G+G++ A Sbjct: 12 ANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRHVEQGRGEQTA 71 Query: 127 IIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQAIYAMLACAR 186 IIYDSP+T TK ISY E+ +V+ LAG L +GV+KGD V+IYMPMIP+A+ AMLACAR Sbjct: 72 IIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPEALEAMLACAR 131 Query: 187 IGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEALRIGQHKPD 246 +GA+HS++FGGFA+ EL+ RID PK ++ AS G+EPGR V Y PLL+ A+ + HKPD Sbjct: 132 LGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDGAIDLATHKPD 191 Query: 247 RLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLPKGVV 306 +I+ R E L+ GRD++W + +CVPV HP YILYTSGTTG PKGV+ Sbjct: 192 FCVIFQR-EQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSGTTGQPKGVI 250 Query: 307 RPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYEGKPV 366 R T G V LNWTM +IY + PG+V+WAASD+GWVVGHSYICYGPL+HGNTT+++EGKP+ Sbjct: 251 RHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTTIVFEGKPI 310 Query: 367 GTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAGERCDV 426 GTPDAG ++RV++EH V + FTAPTA RA++++DP K+Y L+ K +++AGER D Sbjct: 311 GTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQVYLAGERADP 370 Query: 427 ETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGKCVPGYNVMILDDN 486 +T+ W+++ +VPV+DHWWQTETG I A+ +G+ T G +PGY V ILD+ Sbjct: 371 DTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPT-KLGSPAVPMPGYTVDILDEG 429 Query: 487 MQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDEEGYLY 546 + LG I VKLPLPPG LW ++ FK Y FPGYY+T DAG DE+GYLY Sbjct: 430 GHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGMKDEDGYLY 489 Query: 547 VMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLALCVLKKDVNA 606 +M+R DDVINVAGHR+S GA+EE + H V +CAV+G D LKG P+ L + Sbjct: 490 IMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFLCLNAGCDT 549 Query: 607 TEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNGKPYKVTPTI 666 E V+ ++VK VR+ IGPVAAF+ A V +LPKTRSGKI R T+ + +G +K+ TI Sbjct: 550 PHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGTDWKMPATI 609 Query: 667 EDPSIFGHIEEVLK 680 +DP+I I L+ Sbjct: 610 DDPAILDEITTALQ 623 Lambda K H 0.318 0.136 0.421 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: 1356 Number of extensions: 52 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: 683 Length of database: 629 Length adjustment: 38 Effective length of query: 645 Effective length of database: 591 Effective search space: 381195 Effective search space used: 381195 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