Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF1244 PGA1_c12600 biotin carboxylase AccA
Query= BRENDA::Q42523 (734 letters) >FitnessBrowser__Phaeo:GFF1244 Length = 450 Score = 425 bits (1093), Expect = e-123 Identities = 218/443 (49%), Positives = 289/443 (65%), Gaps = 4/443 (0%) Query: 39 EKILVANRGEIACRIMRTAKRLGIQTVAVYSDADRDSLHVKSADEAVRIGPPSARLSYLS 98 +KIL+ANRGEIA R++R + +GIQ+VAV+S AD D++HV+ ADE+V IGPPS SYLS Sbjct: 3 DKILIANRGEIALRVIRACREMGIQSVAVHSTADADAMHVRMADESVCIGPPSGTHSYLS 62 Query: 99 GVTIMEAAARTGAQAIHPGYGFLSESSDFAQLCEDSGLTFIGPPASAIRDMGDKSASKRI 158 I+ A TGAQAIHPGYGFLSE+++F Q+ ED GLTFIGP A IR MGDK +K Sbjct: 63 IPAIISACEITGAQAIHPGYGFLSENANFVQIVEDHGLTFIGPTAEHIRVMGDKITAKDT 122 Query: 159 MGAAGVPLVPGYHGHEQDIDHMKSEAEKIGYPIIIKPTHGGGGKGMRIVQSGKDFADSFL 218 M GVP VPG G D++ K E IGYP+IIK T GGGG+GM++ ++ D +F+ Sbjct: 123 MKDLGVPCVPGSDGGVPDLETAKKIGEDIGYPVIIKATAGGGGRGMKVAKTAADMEQAFM 182 Query: 219 GAQREAAASFGVNTILLEKYITRPRHIEVQIFGDKHGNVLHLYERDCSVQRRHQKIIEEA 278 A+ E A+FG + + +EKY+T PRHIE+Q+FGD G +HL ERDCS+QRRHQK+ EEA Sbjct: 183 TARAEGKAAFGNDEVYIEKYLTTPRHIEIQVFGDGKGKAVHLGERDCSLQRRHQKVFEEA 242 Query: 279 PAPNISEKFRANLGQAAVSAARAVGYYNAGTVEFIVDTESDQFYFMEMNTRLQVEHPVTE 338 P P I+ + RA +G+ A + Y AGT+EF+ E +FYF+EMNTRLQVEHPVTE Sbjct: 243 PGPCITPEERARIGKTCAEAVAKINYIGAGTIEFLY--EKGEFYFIEMNTRLQVEHPVTE 300 Query: 339 MIVGQDLVEWQIRVANGEPLPLSQSEVPMSGHAFEARIYAENVPKGFLPATGVLNHYRPV 398 I G DLV QIRVA G P+ SQ ++ ++GH+ E RI AE +P F P G + Y Sbjct: 301 SIFGVDLVREQIRVAEGLPMSFSQDDLEINGHSIEVRINAEKLP-NFSPCPGRITQYHAP 359 Query: 399 AVSPSVRVETGVEQGDTVSMHYDPMIAKLVVWGGNRGEALVKLKDCLSNFQVAGVPTNIN 458 VR+++ + G ++ +YD +I KL+V G +R EAL +L L V GV T + Sbjct: 360 G-GLGVRMDSALYDGYSIPPYYDSLIGKLIVHGRDRPEALARLSRALGELIVDGVDTTVP 418 Query: 459 FLQKLASHKEFAVGNVETHFIEH 481 L K+ G H++EH Sbjct: 419 LFHALLEEKDIRTGEYNIHWLEH 441 Lambda K H 0.316 0.132 0.386 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: 863 Number of extensions: 35 Number of successful extensions: 3 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: 734 Length of database: 450 Length adjustment: 36 Effective length of query: 698 Effective length of database: 414 Effective search space: 288972 Effective search space used: 288972 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 (21.6 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