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 H281DRAFT_03840 H281DRAFT_03840 urea carboxylase
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Burk376:H281DRAFT_03840 Length = 1199 Score = 328 bits (840), Expect = 9e-94 Identities = 173/439 (39%), Positives = 268/439 (61%), Gaps = 3/439 (0%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F ++L+ANRG IA R+L+ ++E+ +T ++V+SEAD+ + H A A+ +G PA +YL Sbjct: 2 FEKILIANRGAIACRILRTLRELNVTGVSVFSEADRASRHVSEAPIAHELGDGPAAMTYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 + I++ A V AIHPGYGFLSENA F EA E AGI FIGP+ +R K + Sbjct: 62 DSTKILEIARCEGVQAIHPGYGFLSENAAFGEACEAAGIAFIGPTPAQLRAFGLKHTARE 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 +A GVP G+ G + + AL AE IGYP+M+K+ +GGGG+G+ + D+L + Sbjct: 122 IAGEQGVPMLNGT-GLLEDLPAALNAAESIGYPVMLKSTAGGGGIGMRVCWHADELSAHF 180 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 + KRL F + +F+EKY RH+E Q+ GD G+ + R+C++QRRNQK++EE Sbjct: 181 DAVKRLGENNFSDSGVFLEKYIERARHLEVQVFGDGKGDAIALGVRDCSVQRRNQKVLEE 240 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 P+P L +++ + +K K ++Y + GT E + ++ FYFLE+N RLQVEH T Sbjct: 241 TPAPCLPEGIAQALCDAAVKLAKAVDYRSAGTVEFVYDSTAQQFYFLEVNTRLQVEHGVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY- 362 E ++ +DLV+ I+LAAG P ++ + RG AI+ R+ AED +F S G +T+ Sbjct: 301 EQVWGVDLVRWMIELAAGTLAPLNELAASLTPRGHAIQARLYAEDPGRDFIPSPGLLTHV 360 Query: 363 -YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIK 421 + + G +R+D+ IESG VPPY+D +++K+I + +RE A A AL + +I G++ Sbjct: 361 AFPQADGSALRIDTWIESGCEVPPYFDPMLAKIIAWSPTREEARHALNDALQNTRIFGVE 420 Query: 422 TTIELYKWIMQDPDFQEGK 440 T + + I+ D F G+ Sbjct: 421 TNRDYLRQILDDEPFASGE 439 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: 1295 Number of extensions: 56 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: 509 Length of database: 1199 Length adjustment: 41 Effective length of query: 468 Effective length of database: 1158 Effective search space: 541944 Effective search space used: 541944 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: 55 (25.8 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