Align propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_028316428.1 G491_RS0124505 propionyl-CoA synthetase
Query= metacyc::MONOMER-21334 (629 letters) >NCBI__GCF_000429905.1:WP_028316428.1 Length = 639 Score = 847 bits (2188), Expect = 0.0 Identities = 400/627 (63%), Positives = 480/627 (76%) Query: 2 AYQDVYESWKSDPEAFWMEAAKSIDWVEAPSRALDDSNAPLYEWFTDAKVNTCWNAVDRH 61 AY + Y +PE FW A+ W E + LDDSN P Y WF+ NTC+NA+D H Sbjct: 4 AYDEAYRESLENPEEFWGRHAEECFWYEKWDKVLDDSNKPFYRWFSGGVTNTCYNALDMH 63 Query: 62 VEAGRGEQTAIIYDSPITHTKRQISYVELRNRVAMLAGALRAKGVEKGDRVIIYMPMIPE 121 VE G G++ A+IYDSP+T+T ++ +Y ELR+ VA+ AG L GVEKGDRV++YMPMI E Sbjct: 64 VEKGAGDRVALIYDSPVTNTIKKYTYAELRDEVALFAGVLAEYGVEKGDRVVLYMPMIAE 123 Query: 122 ALEAMLACARLGAVHSVVFGGFAANELAVRIDDAQPKAIIAASCGLEPGRVVHYKPLLDG 181 A AMLACARLGAVHSVVFGGFAANELA RI+DA+PKAI++ASCG+E +V+ YKPLLD Sbjct: 124 AAIAMLACARLGAVHSVVFGGFAANELATRINDARPKAIVSASCGIEGKKVIPYKPLLDA 183 Query: 182 AIDMAKHKPEFCVIFQREQEVAHLEEGRDYNWHGFQYGVEPAECVPVEGNHPAYILYTSG 241 AI++++HKP+ C+I QR E A + RD +W P +CVPV P YILYTSG Sbjct: 184 AIEISEHKPKNCMILQRPMETADMHPSRDVDWTEAMKKASPKDCVPVLATDPLYILYTSG 243 Query: 242 TTGAPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNT 301 TTG PKGV+R GH+VAL W+MK +Y+VD GDV+WAASDVGWVVGHSYI Y PL G T Sbjct: 244 TTGQPKGVVRDNGGHMVALKWSMKAVYDVDEGDVWWAASDVGWVVGHSYIVYAPLFKGCT 303 Query: 302 TIVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTAIRAVKREDPKGEMLAKYDLSHLKAL 361 TI+FEGKPVGTPDAG FWRVISEHKVK FTAPTA RA+KREDP ++ YDLS+ K L Sbjct: 304 TILFEGKPVGTPDAGVFWRVISEHKVKCMFTAPTAYRAIKREDPGAALMKNYDLSNFKIL 363 Query: 362 YLAGERADPDTIIWAQKALSVPVIDHWWQTETGWTIAGNPLGIEELPTKLGSPAKAMPGY 421 +LAGER+DPDTI W+++ L VPVIDHWWQTETGW IA N +G+ P K GSP KA+PG+ Sbjct: 364 FLAGERSDPDTITWSERNLGVPVIDHWWQTETGWAIAANCMGLHHFPVKYGSPTKAVPGW 423 Query: 422 DVQILDEGGHQMKPGELGAIAVKLPLPPGTLPGLWNAEARFRKSYLEHFPGYYETGDAGM 481 +VQ+LDE G PG++GA+ VKLPLPPGTLP LW + F YL F GYY T DAG Sbjct: 424 NVQVLDEMGRPAAPGQIGALVVKLPLPPGTLPTLWGNDQAFVNKYLRDFDGYYTTADAGY 483 Query: 482 IDEDGYLYIMARTDDVINVAGHRLSTGGMEEVLAGHEDVAECAVIGVSDDLKGQMPLGFL 541 IDEDGY+Y+MARTDD+INVAGHRLSTG MEEVLA H DVAECAV+GV D LKGQ+PLGFL Sbjct: 484 IDEDGYIYVMARTDDIINVAGHRLSTGAMEEVLADHPDVAECAVLGVEDPLKGQLPLGFL 543 Query: 542 CLNNGCNRDHGDVVKEVVKLVRDKIGPVAAFKLAVVVDRLPKTRSGKILRGTMVSIADGK 601 LN G R + ++VKEVV+++R++IGPV+AFK A VVDRLPKTRSGKILRG M IAD K Sbjct: 544 VLNAGVTRSNDEIVKEVVEMIRERIGPVSAFKTATVVDRLPKTRSGKILRGVMRQIADNK 603 Query: 602 EYKMPATIDDPAILDEIKVALQSLGYA 628 Y+MPATIDDP+IL EI+ AL ++GYA Sbjct: 604 SYRMPATIDDPSILKEIENALNTIGYA 630 Lambda K H 0.319 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: 1397 Number of extensions: 65 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: 639 Length adjustment: 38 Effective length of query: 591 Effective length of database: 601 Effective search space: 355191 Effective search space used: 355191 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Jul 25 2024. The underlying query database was built on Jul 25 2024.
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