Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate Dsui_0982 Dsui_0982 acetyl/propionyl-CoA carboxylase, alpha subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__PS:Dsui_0982 Length = 667 Score = 376 bits (965), Expect = e-108 Identities = 200/449 (44%), Positives = 277/449 (61%), Gaps = 4/449 (0%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 FS++L+ANRGEIA RV+K + +G+ +AVYSEAD A H + ADEA +G A A +SYL Sbjct: 2 FSKILIANRGEIACRVIKTARRLGIRTVAVYSEADANARHVRLADEAVLLGPAAARESYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 E I+DAA + AIHPGYGFLSENA+FAEA AG+ FIGP + +R + K K Sbjct: 62 VAEKILDAARRTGAQAIHPGYGFLSENADFAEACAAAGVVFIGPPASAIRAMGSKSAAKA 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 L A VP PG G + + A+ IGYP+++KAA+GGGG G+ VD + + Sbjct: 122 LMEKAAVPLTPGYHGDNQEPEFLKQQADAIGYPVLIKAAAGGGGKGMRLVDKGEDFIAAL 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 +R A +FG + +EKY PRHIE Q+ GD GN V +ER+C++QRR+QK++EE Sbjct: 182 ASCQREARSSFGNDQVLVEKYITRPRHIEIQVFGDSQGNCVYLFERDCSVQRRHQKVLEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 AP+P + E R M E + K + Y GT E ++ FYF+E+N RLQVEHP T Sbjct: 242 APAPGMTPERRRQMGEAAVAAAKAVGYVGAGTVE-FIANQDGSFYFMEMNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E+I DLV+ Q+++AAGE LP QE L ++RG A+E RI AEDA F S+G + + Sbjct: 301 EMITGQDLVEWQLRVAAGEALPLRQEQL--QIRGHALEARIYAEDAGKGFLPSTGRLLHL 358 Query: 364 REPT-GPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 P G VRVD+G+E G + P+YD +++KLIV+ E RE A+ +ALADY++ G+ T Sbjct: 359 VPPAEGLNVRVDTGVEEGDEITPHYDPMIAKLIVWDEDREAALARMRQALADYRVVGVTT 418 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTD 451 I+ ++ P F T I ++ D Sbjct: 419 NIDFLSRLVSCPAFAGADLDTGLIERQQD 447 Lambda K H 0.317 0.135 0.385 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: 785 Number of extensions: 38 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: 509 Length of database: 667 Length adjustment: 36 Effective length of query: 473 Effective length of database: 631 Effective search space: 298463 Effective search space used: 298463 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