Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate Pf6N2E2_2409 Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4)
Query= metacyc::MONOMER-17283 (535 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2409 Length = 538 Score = 426 bits (1095), Expect = e-123 Identities = 230/549 (41%), Positives = 328/549 (59%), Gaps = 27/549 (4%) Query: 1 MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQG---GGAEQRRRHEERGKLFVR 57 M +I SH+ P+ DF N H ++ A + E+L Q+ Q A+ + + ++RG+L R Sbjct: 1 MPVIESHLDPHCADFTRN---HAAMLAGV-EQLRQLEQAVLEKAAQAQGKFDQRGQLMPR 56 Query: 58 DRIDTLIDPDSSFLEIGALAAYNVYDEE---VPAAGIVCGIGRVAGRPVMIIANDATVKG 114 R++ L+DP + FLE+ +LA Y ++D++ G++ GIG V+G V+++AN++ +KG Sbjct: 57 QRLNLLLDPGAPFLELASLAGYKLHDDKDGSQAGGGLIAGIGYVSGVRVLVVANNSAIKG 116 Query: 115 GTYFPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMS 174 GT P + K LR Q+IA EN+LP I L +SGGA L +++F + R F NQA+MS Sbjct: 117 GTISPSGLYKTLRLQQIAMENKLPVITLAESGGANLNYAAQIFVEG---ARCFANQARMS 173 Query: 175 AEGIPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGG 234 A G+PQI V GS TAGGAY P +SD VV+V+ +FL GPPL+KAATGE + EELGG Sbjct: 174 AMGLPQITVVHGSATAGGAYQPGLSDYVVVVRDKARLFLAGPPLLKAATGEVASEEELGG 233 Query: 235 ADVHTRISGVADYFANDDREALAIVRDIV------AHLGPRQRANWELRDPEPPRYDPRE 288 A +H +++G A+Y A +D + + + R+I+ A L P+ +W P Y E Sbjct: 234 AQMHAQVAGTAEYLAENDADGVRLAREILSLLPWNAQLPPQPERSWT-----EPLYPADE 288 Query: 289 IYGILPRDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGIL 348 + G++P D + YDV+E+IARI DGS FK+ + +CG HI G G++ NNG + Sbjct: 289 LLGLVPDDPKTPYDVQEIIARIADGSNFLAFKSEFDAQTICGHLHIRGHACGLIGNNGPI 348 Query: 349 FSESALKGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPK 408 + A K A FI+LC PL+FL N TGFMVG + E G+ K GAK++ AV+ A VPK Sbjct: 349 TPQGASKAAQFIQLCDQSRTPLLFLHNTTGFMVGTESERQGVIKHGAKMIQAVANARVPK 408 Query: 409 FTVIIGGSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQD 468 TV++GGS+GAGNY MCGR PR ++ WPN+ +VMGG QA VL + G Sbjct: 409 LTVVVGGSYGAGNYAMCGRGLDPRFIFAWPNSHTAVMGGAQAGKVLRMVTEATQIKNGLT 468 Query: 469 MTPEEQERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEA---PV 525 P+ + K + + Y SA LWDDG+IDP +TR +L L EA P+ Sbjct: 469 PDPKVLDLLEQTTAQKLDSQSTALYGSASLWDDGLIDPRDTRTLLGYLLDICHEAEQRPL 528 Query: 526 QPTRFGVFR 534 Q FGV R Sbjct: 529 QANSFGVAR 537 Lambda K H 0.322 0.139 0.423 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: 784 Number of extensions: 48 Number of successful extensions: 5 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: 535 Length of database: 538 Length adjustment: 35 Effective length of query: 500 Effective length of database: 503 Effective search space: 251500 Effective search space used: 251500 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 (21.9 bits) S2: 52 (24.6 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