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 Synpcc7942_1379 Synpcc7942_1379 acetyl-CoA carboxylase biotin carboxylase subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__SynE:Synpcc7942_1379 Length = 453 Score = 406 bits (1044), Expect = e-118 Identities = 213/445 (47%), Positives = 294/445 (66%), Gaps = 3/445 (0%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F+++L+ANRGEIA R+L+ +E+G+ IAV+S D+ A+H + ADEA IG+A + SYL Sbjct: 3 FNKILIANRGEIALRILRTCEELGIGTIAVHSTVDRNALHVQLADEAVCIGEAASSKSYL 62 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 NI +II AA + AIHPGYGFL+ENA FAE +TFIGPS + +R + DK K Sbjct: 63 NIPNIIAAALTRNASAIHPGYGFLAENARFAEICADHHLTFIGPSPDSIRAMGDKSTAKE 122 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 GVPT PGSDG +T +D A K+A +IGYP+M+KA +GGGG G+ V L ++ Sbjct: 123 TMQRVGVPTIPGSDGLLTDVDSAAKVAAEIGYPVMIKATAGGGGRGMRLVREPADLEKLF 182 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 + A AFG L++EK+ PRH+EFQ++ D YGN V ER+C+IQRR+QKL+EE Sbjct: 183 LAAQGEAEAAFGNPGLYLEKFIDRPRHVEFQILADAYGNVVHLGERDCSIQRRHQKLLEE 242 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 APSPAL + R+ M + +K + I Y GT E D + +FYF+E+N R+QVEHP T Sbjct: 243 APSPALSADLRQKMGDAAVKVAQAIGYIGAGTVE-FLVDATGNFYFMEMNTRIQVEHPVT 301 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E+I +DL+ QI++A GE L F Q D+ ++RG AIE RINAED NF + G +T Y Sbjct: 302 EMITGLDLIAEQIRIAQGEALRFRQADI--QLRGHAIECRINAEDPEYNFRPNPGRITGY 359 Query: 364 REPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTT 423 P GPGVRVDS + + +PPYYDSL+ KLIV+G +RE AI RAL + I G+ TT Sbjct: 360 LPPGGPGVRVDSHVYTDYEIPPYYDSLIGKLIVWGATREEAIARMQRALRECAITGLPTT 419 Query: 424 IELYKWIMQDPDFQEGKFSTSYISQ 448 + ++ ++Q P+F G+ T+++ Q Sbjct: 420 LSFHQLMLQMPEFLRGELYTNFVEQ 444 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: 544 Number of extensions: 17 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: 453 Length adjustment: 34 Effective length of query: 475 Effective length of database: 419 Effective search space: 199025 Effective search space used: 199025 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: 51 (24.3 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