Align propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011384701.1 AMB_RS11645 propionyl-CoA synthetase
Query= metacyc::MONOMER-21334 (629 letters) >NCBI__GCF_000009985.1:WP_011384701.1 Length = 638 Score = 867 bits (2240), Expect = 0.0 Identities = 409/628 (65%), Positives = 497/628 (79%) Query: 2 AYQDVYESWKSDPEAFWMEAAKSIDWVEAPSRALDDSNAPLYEWFTDAKVNTCWNAVDRH 61 AYQ YE DPE FW EAAK I W + + LDDS P Y WF A+ NTC+NAVDRH Sbjct: 4 AYQQAYEKSLKDPEGFWGEAAKEIHWYKTWDKVLDDSKKPFYRWFVGAETNTCYNAVDRH 63 Query: 62 VEAGRGEQTAIIYDSPITHTKRQISYVELRNRVAMLAGALRAKGVEKGDRVIIYMPMIPE 121 VE GRG QTAIIYDSP+T TKR+ISY EL+++V+ LAGA+ A GV KGDRV++YMPM+PE Sbjct: 64 VEQGRGAQTAIIYDSPVTSTKRKISYDELKDQVSRLAGAMAALGVAKGDRVLLYMPMVPE 123 Query: 122 ALEAMLACARLGAVHSVVFGGFAANELAVRIDDAQPKAIIAASCGLEPGRVVHYKPLLDG 181 A+ MLA ARLGA+HSVVFGGFA ELA RI+DA+PK I++ASCG+E RV+ YKP+LD Sbjct: 124 AVVGMLAVARLGAIHSVVFGGFAPAELATRINDAKPKVILSASCGIEGSRVIAYKPMLDE 183 Query: 182 AIDMAKHKPEFCVIFQREQEVAHLEEGRDYNWHGFQYGVEPAECVPVEGNHPAYILYTSG 241 AI +++HKP ++ QR Q VA +++ D +W +PA+CVPV P YILYTSG Sbjct: 184 AIALSEHKPGHTIMLQRPQSVAVMDKAGDLDWTEVCAKAKPADCVPVLATDPLYILYTSG 243 Query: 242 TTGAPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNT 301 TTG PKGV+R GH+VAL W+MK +Y++ PG+VFWAASDVGWVVGHSYICY PL++G+T Sbjct: 244 TTGQPKGVVRDNGGHMVALMWSMKYVYDIKPGEVFWAASDVGWVVGHSYICYAPLLNGST 303 Query: 302 TIVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTAIRAVKREDPKGEMLAKYDLSHLKAL 361 T+V+EGKPVGTPDAG FWR+ISE+K+ S FTAPTA RA+KREDP GE+L KYDL+ +AL Sbjct: 304 TVVYEGKPVGTPDAGAFWRMISEYKMASLFTAPTAFRAIKREDPNGELLKKYDLTGFRAL 363 Query: 362 YLAGERADPDTIIWAQKALSVPVIDHWWQTETGWTIAGNPLGIEELPTKLGSPAKAMPGY 421 +LAGER+DPDTI WA++ L VPV+DHWWQTETGW IA N LG+ E P K GSP K +PG+ Sbjct: 364 FLAGERSDPDTINWAREKLKVPVVDHWWQTETGWAIAANCLGLHEFPIKPGSPTKPVPGW 423 Query: 422 DVQILDEGGHQMKPGELGAIAVKLPLPPGTLPGLWNAEARFRKSYLEHFPGYYETGDAGM 481 +++LDEG + G++G++ V+LPLPPG L LWNA+ R SY FPG Y+T DAGM Sbjct: 424 GLEVLDEGHQPCEAGKVGSLVVRLPLPPGALLTLWNADQRCIDSYYSEFPGCYKTADAGM 483 Query: 482 IDEDGYLYIMARTDDVINVAGHRLSTGGMEEVLAGHEDVAECAVIGVSDDLKGQMPLGFL 541 IDEDGY YIM+RTDD+INVAGHRLSTGGMEEVLA H DVAECAVIGV+D LKGQ+PLGF+ Sbjct: 484 IDEDGYAYIMSRTDDIINVAGHRLSTGGMEEVLASHPDVAECAVIGVADQLKGQLPLGFI 543 Query: 542 CLNNGCNRDHGDVVKEVVKLVRDKIGPVAAFKLAVVVDRLPKTRSGKILRGTMVSIADGK 601 CL G + H V+ EVVKLVR+KIGPVAAFK VV+RLPKTRSGKILRGTM IAD + Sbjct: 544 CLKAGVTKPHDQVIAEVVKLVREKIGPVAAFKTCTVVNRLPKTRSGKILRGTMQKIADNQ 603 Query: 602 EYKMPATIDDPAILDEIKVALQSLGYAK 629 ++KMPATIDDP+ILDEI +L+S+GYAK Sbjct: 604 DFKMPATIDDPSILDEIGESLESVGYAK 631 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: 1394 Number of extensions: 66 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: 638 Length adjustment: 38 Effective length of query: 591 Effective length of database: 600 Effective search space: 354600 Effective search space used: 354600 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 Apr 09 2024. The underlying query database was built on Apr 09 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