Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011384701.1 AMB_RS11645 propionyl-CoA synthetase
Query= reanno::Phaeo:GFF1175 (629 letters) >NCBI__GCF_000009985.1:WP_011384701.1 Length = 638 Score = 864 bits (2232), Expect = 0.0 Identities = 409/628 (65%), Positives = 495/628 (78%) Query: 2 SYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRH 61 +Y + YE +PE FW EAA+ I W K L D Y WF A NTCYNAVDRH Sbjct: 4 AYQQAYEKSLKDPEGFWGEAAKEIHWYKTWDKVLDDSKKPFYRWFVGAETNTCYNAVDRH 63 Query: 62 VEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPE 121 VEQGRG QTAIIYDSP+T TKR+ISY EL+++V+ LAGA+ A GV KGDRV++YMPM+PE Sbjct: 64 VEQGRGAQTAIIYDSPVTSTKRKISYDELKDQVSRLAGAMAALGVAKGDRVLLYMPMVPE 123 Query: 122 ALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDG 181 A+ MLA ARLGA+HSVVFGGFA ELA RI+DA PK I++ASCG+E R + YKP+LD Sbjct: 124 AVVGMLAVARLGAIHSVVFGGFAPAELATRINDAKPKVILSASCGIEGSRVIAYKPMLDE 183 Query: 182 AIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSG 241 AI L+ HKP ++ QR Q VA + + D++W +PA+CVPV P YILYTSG Sbjct: 184 AIALSEHKPGHTIMLQRPQSVAVMDKAGDLDWTEVCAKAKPADCVPVLATDPLYILYTSG 243 Query: 242 TTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNT 301 TTGQPKGV+R G +VAL W+MK +Y++ PG+VFWAASDVGWVVGHSYICY PL++G+T Sbjct: 244 TTGQPKGVVRDNGGHMVALMWSMKYVYDIKPGEVFWAASDVGWVVGHSYICYAPLLNGST 303 Query: 302 TIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQV 361 T+V+EGKP+GTPDAG FWR+ISE+K+ S FTAPTAFRA+KREDP GE +KKYDL+ + + Sbjct: 304 TVVYEGKPVGTPDAGAFWRMISEYKMASLFTAPTAFRAIKREDPNGELLKKYDLTGFRAL 363 Query: 362 YLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPGY 421 +LAGER+DPDTI WA+E+LKVPV+DHWWQTETGW+IAAN LG+ E P K GSP P+PG+ Sbjct: 364 FLAGERSDPDTINWAREKLKVPVVDHWWQTETGWAIAANCLGLHEFPIKPGSPTKPVPGW 423 Query: 422 TVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGM 481 +++LDEG P G++G++ V+LPLPPG L TLWNA+ R SY + FPG Y+T DAGM Sbjct: 424 GLEVLDEGHQPCEAGKVGSLVVRLPLPPGALLTLWNADQRCIDSYYSEFPGCYKTADAGM 483 Query: 482 KDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFL 541 DEDGY YIM+RTDD+INVAGHRLSTG MEEVLA HPDVAECAVIGV+D LKGQ P+GF+ Sbjct: 484 IDEDGYAYIMSRTDDIINVAGHRLSTGGMEEVLASHPDVAECAVIGVADQLKGQLPLGFI 543 Query: 542 CLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGT 601 CL AG PH+ V+A+VVKLVREKIGPVAAFK VV+RLPKTRSGKILRGTM IAD Sbjct: 544 CLKAGVTKPHDQVIAEVVKLVREKIGPVAAFKTCTVVNRLPKTRSGKILRGTMQKIADNQ 603 Query: 602 DWKMPATIDDPAILDEITTALQGLGYAK 629 D+KMPATIDDP+ILDEI +L+ +GYAK Sbjct: 604 DFKMPATIDDPSILDEIGESLESVGYAK 631 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: 1368 Number of extensions: 57 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 ( 7.3 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