Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate PfGW456L13_2287 Geranyl-CoA carboxylase carboxyl transferase subunit
Query= BRENDA::Q9I297 (535 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2287 Length = 538 Score = 461 bits (1186), Expect = e-134 Identities = 248/541 (45%), Positives = 336/541 (62%), Gaps = 11/541 (2%) Query: 1 MAILHTQINPRSAEFAANAATMLEQVNALRTLLGRIHEGGGSAAQARHSARGKLLVRERI 60 M ++ +Q++P S FA N A ML + +R L + A + + RG+LL RER+ Sbjct: 1 MPVIQSQLDPHSESFAQNRAAMLSAIEQVRVLEQNLLNKAAEA-RPKFEKRGQLLPRERL 59 Query: 61 NRLLDPGSPFLELSALAAHEVYGEE---VAAAGIVAGIGRVEGVECMIVGNDATVKGGTY 117 N LLDPG+PFLEL++LA ++++ ++ A G++AGIG V GV ++V N++ ++GGT Sbjct: 60 NLLLDPGAPFLELASLAGYKLHDDKDGSSAGGGLIAGIGYVSGVRVLVVANNSAIRGGTI 119 Query: 118 YPLTVKKHLRAQAIALENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSARG 177 P +KK LR Q IA+EN+LP I L +SGGANL E+F + R F NQA MSA G Sbjct: 120 SPSGLKKSLRLQQIAMENKLPVITLAESGGANLNYAAEIFVEG---ARSFANQARMSAMG 176 Query: 178 IPQIAVVMGSCTAGGAYVPAMSDETVMVREQATIFLAGPPLVKAATGEVVSAEELGGADV 237 +PQ+ VV GS TAGGAY P +SD V+VR +A +FLAGPPL+KAATGEV + EELGGA++ Sbjct: 177 LPQVTVVHGSATAGGAYQPGLSDYVVVVRGKAKLFLAGPPLLKAATGEVATDEELGGAEM 236 Query: 238 HCKVSGVADHYAEDDDHALAIARRCVANLNWRKQ-GQLQCRAPRAPLYPAEELYGVIPAD 296 H + +G A++ AE+D + R ++ L W +Q L R PLYP +EL G+IP D Sbjct: 237 HAQTAGTAEYLAENDADGVRQVREIISLLPWNEQLPPLPERRWEEPLYPIDELLGLIPDD 296 Query: 297 SKQPYDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKG 356 K+PYD RE+IARL D S F EFK F +CG + G + NNG + + A K Sbjct: 297 PKKPYDAREIIARLADASNFLEFKGEFDQQTLCGHLKIQGRACGFIGNNGPITPKGASKA 356 Query: 357 AHFIELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACARVPKFTVLIGGS 416 A FI+L Q PLLF N TGFMVG + E G+ KHGAK++ AVA ARVPK T+++GGS Sbjct: 357 AQFIQLCDQSQTPLLFFHNTTGFMVGTESEQQGVIKHGAKMIQAVANARVPKLTIVVGGS 416 Query: 417 FGAGNYGMCGRAYDPRFLWMWPNARIGVMGGEQAAGVLAQVKREQAERAGQQLGVEEEAK 476 +GAGNY MCGR DPRF++ WPN+R VMGG QA VL V + + G + Sbjct: 417 YGAGNYAMCGRGLDPRFIFAWPNSRTAVMGGAQAGKVLRIVTEAKQAKDGLVPDPKMLDM 476 Query: 477 IKAPILEQYEHQGHPYYSSARLWDDGVIDPAQTREVLALALSAALNA---PIEPTAFGVF 533 ++ ++ + Q Y SA LWDDG+IDP TR +L L A P++ +FGV Sbjct: 477 LEQVTAQKLDSQSTALYGSANLWDDGLIDPRDTRTLLGYLLDICHEAEVRPLQANSFGVA 536 Query: 534 R 534 R Sbjct: 537 R 537 Lambda K H 0.321 0.137 0.409 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: 764 Number of extensions: 35 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