Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate AO356_02920 AO356_02920 acetyl-CoA carboxylase carboxyltransferase subunit
Query= metacyc::MONOMER-17283 (535 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_02920 Length = 538 Score = 428 bits (1101), Expect = e-124 Identities = 230/546 (42%), Positives = 325/546 (59%), Gaps = 21/546 (3%) Query: 1 MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60 M +I SH+ P+S DF N A + LR+ L + A+ + + ++RG+L R R+ Sbjct: 1 MPVIESHLDPHSADFARNHAAMLAGVEQLRQ-LERAVLAKAAQAQDKFDQRGQLLPRQRL 59 Query: 61 DTLIDPDSSFLEIGALAAYNVYDEE---VPAAGIVCGIGRVAGRPVMIIANDATVKGGTY 117 + L+DP + FLE+ +LA Y ++D++ G++ GIG V+G +++AN++ +KGGT Sbjct: 60 NLLLDPGAPFLELASLAGYKLHDDKDGSQAGGGLIAGIGYVSGVRALVVANNSAIKGGTI 119 Query: 118 FPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEG 177 P + K LR Q+IA EN+LP I L +SGGA L +++F + R F NQA+MSA G Sbjct: 120 SPSGLHKTLRLQQIAMENKLPVITLAESGGANLNYAAQIFVEG---ARCFANQARMSAMG 176 Query: 178 IPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADV 237 +PQI V GS TAGGAY P +SD VV+V+ +FL GPPL+KAATGE + EELGGA + Sbjct: 177 LPQITVVHGSATAGGAYQPGLSDYVVVVRDKARLFLAGPPLLKAATGEVASEEELGGALM 236 Query: 238 HTRISGVADYFANDDREALAIVRDIV------AHLGPRQRANWELRDPEPPRYDPREIYG 291 H +++G A+Y A +D + + + R+I+ A L P+ W P Y E+ G Sbjct: 237 HVQVAGTAEYLAENDADGIRLAREILDLLPWNAQLPPQPERTWT-----EPLYPADELLG 291 Query: 292 ILPRDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSE 351 ++P D ++ YDV E+IARI DGS FK+ + T +CG HI G G++ NNG + + Sbjct: 292 LVPDDPKKPYDVGEIIARIADGSHFLAFKSEFDTQTICGHLHIRGHTCGLIGNNGPITPQ 351 Query: 352 SALKGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTV 411 A K A FI+LC PL+FL N TGFMVG + E G+ K GAK++ AV+ A VPK TV Sbjct: 352 GAAKAAQFIQLCDQSRTPLLFLHNTTGFMVGTESERQGVIKHGAKMIQAVANARVPKLTV 411 Query: 412 IIGGSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTP 471 ++GGS+GAGNY MCGR PR ++ WPN+ +VMGG QA VL + G P Sbjct: 412 VVGGSYGAGNYAMCGRGLDPRFIFAWPNSHTAVMGGAQAGKVLRMVTEATQLKNGLSPDP 471 Query: 472 EEQERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEA---PVQPT 528 + + K + + Y SA LWDDG+IDP +TR +L L L EA P+Q Sbjct: 472 KMLDLLEQTTAQKLDSQSTALYGSASLWDDGLIDPRDTRTLLGLLLDICHEAEQRPLQAN 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: 786 Number of extensions: 44 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