Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Pf6N2E2_2409 Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4)
Query= BRENDA::Q9I297 (535 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2409 Length = 538 Score = 471 bits (1211), Expect = e-137 Identities = 252/541 (46%), Positives = 342/541 (63%), Gaps = 11/541 (2%) Query: 1 MAILHTQINPRSAEFAANAATMLEQVNALRTLLGRIHEGGGSAAQARHSARGKLLVRERI 60 M ++ + ++P A+F N A ML V LR L + E A Q + RG+L+ R+R+ Sbjct: 1 MPVIESHLDPHCADFTRNHAAMLAGVEQLRQLEQAVLEKAAQA-QGKFDQRGQLMPRQRL 59 Query: 61 NRLLDPGSPFLELSALAAHEVYGEE---VAAAGIVAGIGRVEGVECMIVGNDATVKGGTY 117 N LLDPG+PFLEL++LA ++++ ++ A G++AGIG V GV ++V N++ +KGGT Sbjct: 60 NLLLDPGAPFLELASLAGYKLHDDKDGSQAGGGLIAGIGYVSGVRVLVVANNSAIKGGTI 119 Query: 118 YPLTVKKHLRAQAIALENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSARG 177 P + K LR Q IA+EN+LP I L +SGGANL ++F + R F NQA MSA G Sbjct: 120 SPSGLYKTLRLQQIAMENKLPVITLAESGGANLNYAAQIFVEG---ARCFANQARMSAMG 176 Query: 178 IPQIAVVMGSCTAGGAYVPAMSDETVMVREQATIFLAGPPLVKAATGEVVSAEELGGADV 237 +PQI VV GS TAGGAY P +SD V+VR++A +FLAGPPL+KAATGEV S EELGGA + Sbjct: 177 LPQITVVHGSATAGGAYQPGLSDYVVVVRDKARLFLAGPPLLKAATGEVASEEELGGAQM 236 Query: 238 HCKVSGVADHYAEDDDHALAIARRCVANLNWRKQGQLQC-RAPRAPLYPAEELYGVIPAD 296 H +V+G A++ AE+D + +AR ++ L W Q Q R+ PLYPA+EL G++P D Sbjct: 237 HAQVAGTAEYLAENDADGVRLAREILSLLPWNAQLPPQPERSWTEPLYPADELLGLVPDD 296 Query: 297 SKQPYDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKG 356 K PYDV+E+IAR+ DGS F FK+ F +CG H+ G+ ++ NNG + + A K Sbjct: 297 PKTPYDVQEIIARIADGSNFLAFKSEFDAQTICGHLHIRGHACGLIGNNGPITPQGASKA 356 Query: 357 AHFIELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACARVPKFTVLIGGS 416 A FI+L Q PLLFL N TGFMVG + E G+ KHGAK++ AVA ARVPK TV++GGS Sbjct: 357 AQFIQLCDQSRTPLLFLHNTTGFMVGTESERQGVIKHGAKMIQAVANARVPKLTVVVGGS 416 Query: 417 FGAGNYGMCGRAYDPRFLWMWPNARIGVMGGEQAAGVLAQVKREQAERAGQQLGVEEEAK 476 +GAGNY MCGR DPRF++ WPN+ VMGG QA VL V + G + Sbjct: 417 YGAGNYAMCGRGLDPRFIFAWPNSHTAVMGGAQAGKVLRMVTEATQIKNGLTPDPKVLDL 476 Query: 477 IKAPILEQYEHQGHPYYSSARLWDDGVIDPAQTREVLALALSAALNA---PIEPTAFGVF 533 ++ ++ + Q Y SA LWDDG+IDP TR +L L A P++ +FGV Sbjct: 477 LEQTTAQKLDSQSTALYGSASLWDDGLIDPRDTRTLLGYLLDICHEAEQRPLQANSFGVA 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: 788 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