Align propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate 6937194 Sama_1364 acyl-coenzyme A synthetase/AMP-(fatty) acid ligase (RefSeq)
Query= metacyc::MONOMER-21334 (629 letters) >FitnessBrowser__SB2B:6937194 Length = 644 Score = 777 bits (2007), Expect = 0.0 Identities = 370/617 (59%), Positives = 458/617 (74%) Query: 11 KSDPEAFWMEAAKSIDWVEAPSRALDDSNAPLYEWFTDAKVNTCWNAVDRHVEAGRGEQT 70 + +PE +W +AA +DW +APS LD S APLY W+TD ++NTC+NA+DR V+AGRG QT Sbjct: 23 RDNPEQYWRKAADMVDWHKAPSTILDSSQAPLYRWYTDGEINTCYNALDRQVDAGRGSQT 82 Query: 71 AIIYDSPITHTKRQISYVELRNRVAMLAGALRAKGVEKGDRVIIYMPMIPEALEAMLACA 130 A Y SP+T T+ ISY E +V LAG L+A+GV KGDRV+IYMPM+PE AMLACA Sbjct: 83 AFHYVSPVTETEYSISYTECLAQVKRLAGLLKAQGVNKGDRVVIYMPMVPETAYAMLACA 142 Query: 131 RLGAVHSVVFGGFAANELAVRIDDAQPKAIIAASCGLEPGRVVHYKPLLDGAIDMAKHKP 190 R+GA+HSVVFGGFAANELA RI+DA+P +++ASCG+EP VV YKPLLD A+ A HK Sbjct: 143 RIGAIHSVVFGGFAANELASRINDAKPVMVLSASCGVEPSGVVAYKPLLDAALAQASHKV 202 Query: 191 EFCVIFQREQEVAHLEEGRDYNWHGFQYGVEPAECVPVEGNHPAYILYTSGTTGAPKGVL 250 C+I QR Q A + GRD +W A+ VPV+ P Y+LYTSGTTG PKGV+ Sbjct: 203 SKCLILQRPQYEAAMTPGRDLDWQESVASAADADWVPVKATDPLYVLYTSGTTGQPKGVV 262 Query: 251 RPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTTIVFEGKPV 310 R GH VAL W+M+ +Y+++PGD FWAASDVGWVVGHSYI YGPLI G T++++EGKPV Sbjct: 263 RDNGGHAVALAWSMRYLYDIEPGDTFWAASDVGWVVGHSYIVYGPLIAGATSVLYEGKPV 322 Query: 311 GTPDAGTFWRVISEHKVKSFFTAPTAIRAVKREDPKGEMLAKYDLSHLKALYLAGERADP 370 GTPDAG FWR I ++ VKSFFTAPTAIRA+KREDP+G +L LK ++LAGER DP Sbjct: 323 GTPDAGAFWRTIKKYGVKSFFTAPTAIRAIKREDPEGFFCRNTNLDCLKQMFLAGERCDP 382 Query: 371 DTIIWAQKALSVPVIDHWWQTETGWTIAGNPLGIEELPTKLGSPAKAMPGYDVQILDEGG 430 DT++WAQ+ L PVIDHWWQTETGW +A N +GI ++P K GSPA+ +PGY V ++DE G Sbjct: 383 DTLLWAQEMLGKPVIDHWWQTETGWPVASNLMGIAQMPIKPGSPARPVPGYQVDVVDEAG 442 Query: 431 HQMKPGELGAIAVKLPLPPGTLPGLWNAEARFRKSYLEHFPGYYETGDAGMIDEDGYLYI 490 + + GE G + ++LPLPPGTLP LW + R+ SYL +P Y TGDAG +DEDGYLYI Sbjct: 443 NSVGAGEYGNVVIRLPLPPGTLPTLWQNDKRYIDSYLSMYPDCYLTGDAGYMDEDGYLYI 502 Query: 491 MARTDDVINVAGHRLSTGGMEEVLAGHEDVAECAVIGVSDDLKGQMPLGFLCLNNGCNRD 550 M+R DDVINVAGHRLSTG EEVL H VAE AVIGV D LKGQ+PLG + L NG + Sbjct: 503 MSRIDDVINVAGHRLSTGRFEEVLCQHPAVAEAAVIGVEDKLKGQVPLGLVVLKNGVDIT 562 Query: 551 HGDVVKEVVKLVRDKIGPVAAFKLAVVVDRLPKTRSGKILRGTMVSIADGKEYKMPATID 610 + KE+V LVR +IGPVAAFKL + +LPKTRSGKILR TM IAD +EY +PATI+ Sbjct: 563 DEQLNKELVALVRSEIGPVAAFKLVSAIPKLPKTRSGKILRATMRKIADNQEYSVPATIE 622 Query: 611 DPAILDEIKVALQSLGY 627 DPA L+ ++ L +GY Sbjct: 623 DPATLELVRNTLTRMGY 639 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: 1338 Number of extensions: 59 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: 644 Length adjustment: 38 Effective length of query: 591 Effective length of database: 606 Effective search space: 358146 Effective search space used: 358146 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