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 SMc01345 SMc01345 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::Q2QMG2 (737 letters) >FitnessBrowser__Smeli:SMc01345 Length = 449 Score = 422 bits (1086), Expect = e-122 Identities = 218/445 (48%), Positives = 299/445 (67%), Gaps = 5/445 (1%) Query: 39 VEKVLVANRGEIACRVMRTARRLGIPTVAVYSDADRGALHVRAADEAVRLGPPPARESYL 98 + K+L+ANRGEIA RV+R + LGI TVAV+S AD A+HVR ADE+V +GPPP+RESYL Sbjct: 4 ISKILIANRGEIALRVLRACKELGIATVAVHSTADSDAMHVRLADESVCIGPPPSRESYL 63 Query: 99 NASAIVDAALRTGAKAIHPGYGFLSESADFAQLCKAEGLTFIGPPPSAIRDMGDKSASKR 158 N IV A TGA A+HPGYGFLSE+A FA + A G+TFIGP IR MGDK +K+ Sbjct: 64 NIHQIVAACEITGADAVHPGYGFLSENAKFADILDAHGITFIGPTAEHIRLMGDKITAKK 123 Query: 159 IMGAAGVPLVPGYHGAEQDIELLKLEANKIGYPVLIKPTHGGGGKGMRIVQRPEDFVDSV 218 G+P+VPG G + L++ A +IG+PVLIK T GGGG+GM++ + E+ ++V Sbjct: 124 TAEELGIPVVPGSDGEVRPENALEI-ARQIGFPVLIKATAGGGGRGMKVARTEEELENAV 182 Query: 219 LSAQREAAASFGINTLLVEKYITQPRHIEVQIFGDQHGNVIHLYERDCSLQRRHQKIIEE 278 +A+ EAAA+FG + + +EK++ +PRHIE+Q+ GD GN IHL ERDCSLQRRHQK+ EE Sbjct: 183 ATARSEAAAAFGNDAVYMEKFLGKPRHIEIQVVGDGEGNAIHLGERDCSLQRRHQKVWEE 242 Query: 279 APAPNVTAQFRSHIGEAAVSAAKAVGYYSAGTVEFIVDTLSGEFYFMEMNTRLQVEHPVT 338 A +P + + R IG+ A K + Y AGT+EF+ + +GEFYF+EMNTRLQVEHP+T Sbjct: 243 ANSPALNVEQRMKIGQVCADAMKKLKYRGAGTIEFLYE--NGEFYFIEMNTRLQVEHPIT 300 Query: 339 EMIVGQDLVEWQIRIANGECLPLSQEQVPLNGHAFEARIYAENVPRGFLPATGTLHHYRP 398 E I G DLV QIR+A+G L QE + +GHA E RI AE+ PR F+P+ GT+ H+ Sbjct: 301 EAITGIDLVHEQIRVASGAGLSAKQEDIVFSGHAIECRINAED-PRTFVPSPGTITHFH- 358 Query: 399 VPSTATVRVETGVEEGDTVSMHYDPMIAKLVVWGESRNAALVKLKNSLSNFQIAGLPTNV 458 P VRV++G +G + +YD +I KL+V G +R +++L+ L F I G+ T + Sbjct: 359 APGGLGVRVDSGAYQGYRIPPYYDSLIGKLIVHGRTRVECMMRLRRVLDEFVIDGIKTTL 418 Query: 459 GFLQELAGHSAFEKGLVDTHFIERY 483 Q+L + G D H++E + Sbjct: 419 PLFQDLINNQDIANGDYDIHWLEHH 443 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: 710 Number of extensions: 28 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: 737 Length of database: 449 Length adjustment: 36 Effective length of query: 701 Effective length of database: 413 Effective search space: 289513 Effective search space used: 289513 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