Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate 5210124 Shew_2568 AMP-dependent synthetase and ligase (RefSeq)
Query= reanno::Phaeo:GFF1175 (629 letters) >FitnessBrowser__PV4:5210124 Length = 662 Score = 813 bits (2100), Expect = 0.0 Identities = 389/616 (63%), Positives = 468/616 (75%) Query: 13 NPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRHVEQGRGEQTAI 72 NP FW EAA A++WD + L D +Y WF+ ++NTCYNAVDRHVE GRGEQ AI Sbjct: 43 NPNAFWGEAAGALAWDKTFERVLDDSQAPMYRWFSGGQLNTCYNAVDRHVEAGRGEQVAI 102 Query: 73 IYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPEALEAMLACARL 132 Y SPIT T+ I+Y EL+ +V+ LAG + ++GV KGDRVIIYMPM+PE AMLACARL Sbjct: 103 QYVSPITGTEYGITYNELQAQVSRLAGYMASQGVVKGDRVIIYMPMVPETAYAMLACARL 162 Query: 133 GAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDGAIDLATHKPDF 192 GA+HSVVFGGFAANELA RIDDATPK I++ASCG+EP V YKPLLD A++ A+HK + Sbjct: 163 GAIHSVVFGGFAANELATRIDDATPKMILSASCGVEPSGVVAYKPLLDDALEQASHKVEQ 222 Query: 193 CVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSGTTGQPKGVIRH 252 CVI R Q A+L++GRDV+W G EC VE P YILYTSGTTGQPKGV+R Sbjct: 223 CVILNRPQLQADLVDGRDVDWQGAMADAPNIECQTVEATDPLYILYTSGTTGQPKGVVRD 282 Query: 253 TAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTTIVFEGKPIGT 312 G VAL W+MK+IY++DPGDVFWAASDVGWVVGHSYI YGPL+ G TT++FEGKP+GT Sbjct: 283 NGGHAVALAWSMKHIYDIDPGDVFWAASDVGWVVGHSYIVYGPLLVGATTVLFEGKPVGT 342 Query: 313 PDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQVYLAGERADPDT 372 PD G FWR I+++ VKSFFTAPTA RA+KR+DP+G+++K DLSCL ++LAGER DPDT Sbjct: 343 PDPGIFWRTIAKYNVKSFFTAPTAIRAIKRDDPEGDYLKDVDLSCLGTLFLAGERCDPDT 402 Query: 373 ITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPGYTVDILDEGGHP 432 + WA++QL PVIDHWWQTETGW +AAN +G +P K GSPA +PGY V +LDE G Sbjct: 403 LHWAEQQLDKPVIDHWWQTETGWPVAANLMGTAPVPVKAGSPAKAVPGYDVQVLDEMGDV 462 Query: 433 VAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGMKDEDGYLYIMA 492 VAP + G + +KLPLPPGTL TLW E R+K+SYL+ +PGYY TGDAG DEDGYLYIM+ Sbjct: 463 VAPDQSGNVVIKLPLPPGTLATLWQNEGRYKESYLSMYPGYYLTGDAGYMDEDGYLYIMS 522 Query: 493 RTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFLCLNAGCDTPHE 552 R DD+INVAGHRLSTG EEVL H VAE AVIGV D LKGQ P+G + L GCD E Sbjct: 523 RIDDIINVAGHRLSTGRFEEVLCQHEAVAEAAVIGVDDKLKGQVPLGLVVLKKGCDLSDE 582 Query: 553 DVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGTDWKMPATIDDP 612 + +++ LVRE+IGPVAAFKL V +LPKTRSGKILRGTM IAD ++KMPATI+DP Sbjct: 583 QLYKELIALVREQIGPVAAFKLVSAVPKLPKTRSGKILRGTMRKIADNQEFKMPATIEDP 642 Query: 613 AILDEITTALQGLGYA 628 L+ + AL +GYA Sbjct: 643 YTLELVRNALTRMGYA 658 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: 1403 Number of extensions: 61 Number of successful extensions: 1 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: 662 Length adjustment: 38 Effective length of query: 591 Effective length of database: 624 Effective search space: 368784 Effective search space used: 368784 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