Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate PP_0558 PP_0558 acetyl-CoA carboxylase - biotin carboxylase subunit
Query= SwissProt::Q2QMG2 (737 letters) >FitnessBrowser__Putida:PP_0558 Length = 451 Score = 407 bits (1045), Expect = e-118 Identities = 208/446 (46%), Positives = 295/446 (66%), Gaps = 5/446 (1%) Query: 37 GAVEKVLVANRGEIACRVMRTARRLGIPTVAVYSDADRGALHVRAADEAVRLGPPPARES 96 G +EKVL+ANRGEIA R++R + LGI TVAV+S ADR +H+ ADE+V +GP +++S Sbjct: 3 GKLEKVLIANRGEIALRILRACKELGIKTVAVHSTADRELMHLGLADESVCIGPASSKDS 62 Query: 97 YLNASAIVDAALRTGAKAIHPGYGFLSESADFAQLCKAEGLTFIGPPPSAIRDMGDKSAS 156 YL+ AI+ AA TGA AIHPGYGFL+E+ADFA+ + G FIGP IR MGDK ++ Sbjct: 63 YLHIPAIIAAAEVTGATAIHPGYGFLAENADFAEQVEKSGFAFIGPKADTIRLMGDKVSA 122 Query: 157 KRIMGAAGVPLVPGYHG-AEQDIELLKLEANKIGYPVLIKPTHGGGGKGMRIVQRPEDFV 215 K M +GVP VPG G +D E+ A +GYPV+IK GGGG+GMR+V + ED + Sbjct: 123 KDAMIKSGVPTVPGSDGPLPEDEEVALAIARDVGYPVIIKAAGGGGGRGMRVVHKEEDLI 182 Query: 216 DSVLSAQREAAASFGINTLLVEKYITQPRHIEVQIFGDQHGNVIHLYERDCSLQRRHQKI 275 S + EA A+FG + +EK++T PRH+EVQ+ D GN IHL +RDCSLQRRHQK+ Sbjct: 183 SSAKLTRTEAGAAFGNPMVYLEKFLTNPRHVEVQVLSDGQGNAIHLGDRDCSLQRRHQKV 242 Query: 276 IEEAPAPNVTAQFRSHIGEAAVSAAKAVGYYSAGTVEFIVDTLSGEFYFMEMNTRLQVEH 335 +EEAPAP + + R + + V A +GY AGT EF+ + +G FYF+EMNTR+QVEH Sbjct: 243 LEEAPAPGIDEKARQEVFKRCVDACIEIGYRGAGTFEFLYE--NGRFYFIEMNTRVQVEH 300 Query: 336 PVTEMIVGQDLVEWQIRIANGECLPLSQEQVPLNGHAFEARIYAENVPRGFLPATGTLHH 395 PV+EM+ G D+V+ + IA G L QE V + GH+ E RI AE+ P+ F+P+ G + H Sbjct: 301 PVSEMVTGIDIVKEMLSIAAGNKLSFRQEDVVIRGHSLECRINAED-PKKFIPSPGKVKH 359 Query: 396 YRPVPSTATVRVETGVEEGDTVSMHYDPMIAKLVVWGESRNAALVKLKNSLSNFQIAGLP 455 + P VRV++ + G +V +YD +I KL+ +G+ R+ A+ +++N+L + G+ Sbjct: 360 FH-APGGNGVRVDSHLYSGYSVPPNYDSLIGKLITYGKDRDEAMARMRNALDEIVVDGIK 418 Query: 456 TNVGFLQELAGHSAFEKGLVDTHFIE 481 TN+ ++L F KG V+ H++E Sbjct: 419 TNIPLHRDLVRDEGFCKGGVNIHYLE 444 Lambda K H 0.317 0.133 0.389 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: 735 Number of extensions: 32 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: 737 Length of database: 451 Length adjustment: 36 Effective length of query: 701 Effective length of database: 415 Effective search space: 290915 Effective search space used: 290915 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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