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 WP_053939334.1 WG78_RS18565 urea carboxylase
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_001294205.1:WP_053939334.1 Length = 1216 Score = 352 bits (903), Expect = e-101 Identities = 189/445 (42%), Positives = 277/445 (62%), Gaps = 5/445 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F+ VL+ANRGEIA R ++ +K +G+ ++AV+S+AD+ + H AD A +G DSYL Sbjct: 2 FNTVLIANRGEIACRAIRTLKHLGVVSVAVFSDADRNSAHVAQADVAIALGGDRPADSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 I+ IIDA ++ A+ PGYGFLSE+AEFA A + GI FIGP++ M++ K + Sbjct: 62 RIDKIIDACKQTGAQAVFPGYGFLSESAEFAAACDANGIVFIGPTALQMQEFGLKHRARE 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 LA AGVPT PGS G + S+ +AL+ A KIGYP+M+K+ +GGGG+G+TR ++ ++L + Sbjct: 122 LAAQAGVPTTPGS-GLLASVADALEQAGKIGYPVMLKSTAGGGGIGLTRCNSAEELAAAF 180 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 +R +R+ Q F + F+E++ RHIE Q+ GD G ER+C+IQRRNQK+IEE Sbjct: 181 DRVQRMGEQFFRDSGAFVERFVDQARHIEVQIFGDGKGQVAALGERDCSIQRRNQKVIEE 240 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 P+P L R ++ G+ +NY + GT E + +FYFLE+N RLQVEHP T Sbjct: 241 TPAPNLPAATRAALLASAKALGESVNYRSAGTVEYVYDSARDEFYFLEVNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E + +DLV+ +++AAG+ L + + LN +G AIE R+ AED + F S G +T Sbjct: 301 ESVTGLDLVECMLRVAAGDALDW--DALNAAPQGAAIEVRLYAEDPVKQFQPSPGLLTEV 358 Query: 364 REPTGP--GVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIK 421 R P VRVD +++G+ VP YD L++KLIV G RE A+ +ALA + GI Sbjct: 359 RFPESDIVPVRVDGWVQTGTEVPSLYDPLLAKLIVKGADREQALDNLQKALAHTALHGIA 418 Query: 422 TTIELYKWIMQDPDFQEGKFSTSYI 446 T ++ + I+ F GK ST ++ Sbjct: 419 TNLDYLRQIIASEAFYSGKVSTRFL 443 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: 1279 Number of extensions: 55 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: 1216 Length adjustment: 41 Effective length of query: 468 Effective length of database: 1175 Effective search space: 549900 Effective search space used: 549900 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 24 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