Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate PfGW456L13_2287 Geranyl-CoA carboxylase carboxyl transferase subunit
Query= metacyc::MONOMER-17283 (535 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2287 Length = 538 Score = 422 bits (1086), Expect = e-122 Identities = 231/546 (42%), Positives = 324/546 (59%), Gaps = 21/546 (3%) Query: 1 MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60 M +I S + P+S F N A S +R L Q AE R + E+RG+L R+R+ Sbjct: 1 MPVIQSQLDPHSESFAQNRAAMLSAIEQVRV-LEQNLLNKAAEARPKFEKRGQLLPRERL 59 Query: 61 DTLIDPDSSFLEIGALAAYNVYDEEVPAA---GIVCGIGRVAGRPVMIIANDATVKGGTY 117 + L+DP + FLE+ +LA Y ++D++ ++ G++ GIG V+G V+++AN++ ++GGT Sbjct: 60 NLLLDPGAPFLELASLAGYKLHDDKDGSSAGGGLIAGIGYVSGVRVLVVANNSAIRGGTI 119 Query: 118 FPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEG 177 P +KK LR Q+IA EN+LP I L +SGGA L +E+F + R F NQA+MSA G Sbjct: 120 SPSGLKKSLRLQQIAMENKLPVITLAESGGANLNYAAEIFVEG---ARSFANQARMSAMG 176 Query: 178 IPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADV 237 +PQ+ V GS TAGGAY P +SD VV+V+G +FL GPPL+KAATGE T EELGGA++ Sbjct: 177 LPQVTVVHGSATAGGAYQPGLSDYVVVVRGKAKLFLAGPPLLKAATGEVATDEELGGAEM 236 Query: 238 HTRISGVADYFANDDREALAIVRDIVA------HLGPRQRANWELRDPEPPRYDPREIYG 291 H + +G A+Y A +D + + VR+I++ L P WE P Y E+ G Sbjct: 237 HAQTAGTAEYLAENDADGVRQVREIISLLPWNEQLPPLPERRWE-----EPLYPIDELLG 291 Query: 292 ILPRDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSE 351 ++P D ++ YD RE+IAR+ D S EFK + +CG I+G G + NNG + + Sbjct: 292 LIPDDPKKPYDAREIIARLADASNFLEFKGEFDQQTLCGHLKIQGRACGFIGNNGPITPK 351 Query: 352 SALKGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTV 411 A K A FI+LC PL+F N TGFMVG + E G+ K GAK++ AV+ A VPK T+ Sbjct: 352 GASKAAQFIQLCDQSQTPLLFFHNTTGFMVGTESEQQGVIKHGAKMIQAVANARVPKLTI 411 Query: 412 IIGGSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTP 471 ++GGS+GAGNY MCGR PR ++ WPN+R +VMGG QA VL + G P Sbjct: 412 VVGGSYGAGNYAMCGRGLDPRFIFAWPNSRTAVMGGAQAGKVLRIVTEAKQAKDGLVPDP 471 Query: 472 EEQERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEA---PVQPT 528 + + K + + Y SA LWDDG+IDP +TR +L L EA P+Q Sbjct: 472 KMLDMLEQVTAQKLDSQSTALYGSANLWDDGLIDPRDTRTLLGYLLDICHEAEVRPLQAN 531 Query: 529 RFGVFR 534 FGV R Sbjct: 532 SFGVAR 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: 757 Number of extensions: 36 Number of successful extensions: 4 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