Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate GFF2099 HP15_2053 PrpE protein
Query= reanno::Phaeo:GFF1175 (629 letters) >FitnessBrowser__Marino:GFF2099 Length = 624 Score = 755 bits (1950), Expect = 0.0 Identities = 352/619 (56%), Positives = 455/619 (73%) Query: 1 MSYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDR 60 M Y + P++FW E AE I W P +G +WF D +NTC A+D Sbjct: 1 MDYHSEFRRSIDKPDEFWREQAEKIDWIEPPKTIWQPTDNGHGQWFPDGTLNTCDVALDA 60 Query: 61 HVEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIP 120 ++ GRG+Q A+IYDSP+T T+R +Y EL + VA AGAL+ +G+ KGDRVIIYMPMIP Sbjct: 61 NIRAGRGDQKALIYDSPVTDTQRSYTYNELTDEVARFAGALKDRGITKGDRVIIYMPMIP 120 Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLD 180 EA+ AML CAR+GA+HSVVFGGFAA+ELAVRIDDA PKA+I ASCG+E R + YKPL+D Sbjct: 121 EAVIAMLGCARIGAIHSVVFGGFAAHELAVRIDDAKPKAVITASCGIEVTRVIEYKPLVD 180 Query: 181 GAIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTS 240 AID A+HKP+ C+++QR+Q AEL RD +W+ EPA+ VPV+ P YILYTS Sbjct: 181 KAIDQASHKPETCIVYQRQQVQAELQACRDHDWNELMETAEPADPVPVKSTDPLYILYTS 240 Query: 241 GTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGN 300 GTTG+PKGV+R G VALN++MK +Y+ PGDV+WAASDVGWVVGHSYI Y PL G Sbjct: 241 GTTGKPKGVVRDNGGHAVALNYSMKLVYDAKPGDVYWAASDVGWVVGHSYIVYAPLFAGC 300 Query: 301 TTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQ 360 TTI++EGKP+ TPDAG FWRV+ +HKV FTAPTAFRAV++EDP+ + + +YD+S LK+ Sbjct: 301 TTIMYEGKPVKTPDAGAFWRVVQDHKVNMLFTAPTAFRAVRKEDPEADQLSRYDISSLKR 360 Query: 361 VYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPG 420 ++LAGER DP T W +E +PV+DHWWQTETGW+I NP+GIE + TK GS VP PG Sbjct: 361 LFLAGERLDPATYEWLKEHTGLPVLDHWWQTETGWAICCNPVGIELMATKPGSATVPSPG 420 Query: 421 YTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAG 480 Y V ++D G + GE G IAVKLPLPPG + T+W ++RF+K+YL G+Y +GD G Sbjct: 421 YNVQVVDMNGSQMPAGEQGQIAVKLPLPPGCMMTVWGDDERFRKTYLEPISGFYSSGDGG 480 Query: 481 MKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGF 540 D+DGY+++M RTDDVINVAGHRLSTG MEEV+A HP +AEC V+G D +KGQ P+G Sbjct: 481 FIDDDGYVFVMGRTDDVINVAGHRLSTGEMEEVVASHPAIAECCVVGAHDDMKGQIPIGL 540 Query: 541 LCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600 + + G H+++ ++V++VR+KIG +A F+ A VVDRLPKTRSGKILR + IADG Sbjct: 541 VLIKDGATIDHDELEDELVEMVRDKIGAIACFRRALVVDRLPKTRSGKILRRVIRQIADG 600 Query: 601 TDWKMPATIDDPAILDEIT 619 ++ +P+TIDDPAIL+EI+ Sbjct: 601 EEYSVPSTIDDPAILEEIS 619 Lambda K H 0.318 0.137 0.428 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: 1336 Number of extensions: 58 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: 629 Length of database: 624 Length adjustment: 38 Effective length of query: 591 Effective length of database: 586 Effective search space: 346326 Effective search space used: 346326 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