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 GFF2304 Psest_2351 urea carboxylase
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__psRCH2:GFF2304 Length = 1199 Score = 332 bits (850), Expect = 6e-95 Identities = 176/439 (40%), Positives = 269/439 (61%), Gaps = 3/439 (0%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F ++L+ANRG IA R+L+ ++ + + ++AVYSEAD ++H + ADEA+ +G+ PA +YL Sbjct: 2 FDKLLIANRGAIACRILRTLRGLDVKSVAVYSEADAASLHIQQADEAHSLGEGPAAQTYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 +E I+ A + AIHPGYGFLSENA FAEA E AGI F+GP+ E +R K + Sbjct: 62 VVEKILRIARETGASAIHPGYGFLSENAAFAEACEAAGIAFVGPTPEQLRMFGLKHTARA 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 LA GVP G++ + S+ +AL AE++GYP+M+K+ +GGGG+G+ + +L + + Sbjct: 122 LAKQRGVPMLEGTE-LLDSLADALGAAEQVGYPVMLKSTAGGGGIGMRVCRSAAELAEAF 180 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 + KRL F A +FIEKY RH+E Q+ GD G + R+C++QRRNQK++EE Sbjct: 181 DAVKRLGQNNFSDAGVFIEKYIQRARHLEVQVFGDGRGEVIALGVRDCSVQRRNQKVLEE 240 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 P+P L E++ E +K K ++Y + GT E + + FYFLE+N RLQVEH T Sbjct: 241 TPAPNLPAGMAEALCEAAVKLAKAVSYRSAGTVEFVYDAEAEQFYFLEVNTRLQVEHGVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E ++ +DLV+ I+LAAG+ P + + G +I+ R+ AED +F S G +T Sbjct: 301 EQVWGVDLVRWMIELAAGDLPPLVELARALKSSGHSIQARLYAEDPGRDFQPSPGLLTVV 360 Query: 364 REPTGPG--VRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIK 421 P G G +R+D+ +E+G +PPY+D +V+KLI + RE A A AL + + G++ Sbjct: 361 DFPKGDGKALRIDTWVEAGCEIPPYFDPMVAKLITWAPDRESARAALDTALDETLLYGVE 420 Query: 422 TTIELYKWIMQDPDFQEGK 440 + + I+ F EG+ Sbjct: 421 SNRAYLRQILGYAPFAEGR 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: 1263 Number of extensions: 59 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