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_0389 Dsui_0389 acetyl-CoA carboxylase, biotin carboxylase subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__PS:Dsui_0389 Length = 455 Score = 385 bits (990), Expect = e-111 Identities = 207/447 (46%), Positives = 290/447 (64%), Gaps = 6/447 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F ++L+ANRGEIA RV +A +E+G+ + V+SEAD+ A + K ADE+ IG A + SYL Sbjct: 2 FEKILIANRGEIALRVQRACRELGIKTVVVHSEADREAKYVKLADESVCIGPASSALSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 NI II AAE AIHPGYGFLSENA+FAE VE +G FIGP +E +R + DK+ K Sbjct: 62 NIPAIISAAEVTDAQAIHPGYGFLSENADFAERVESSGFVFIGPRAETIRLMGDKVSAKD 121 Query: 124 LANMAGVPTAPGSDGPV-TSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDV 182 AGVP PGSDG + E +K+ +GYP+++KAA GGGG G+ V + L++ Sbjct: 122 AMKAAGVPCVPGSDGALPEDPKEIIKIGRAVGYPVIIKAAGGGGGRGMRVVHTEAALINA 181 Query: 183 WERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIE 242 ++ A AFG +++EK+ NPRH+E Q++ D++ N V ER+C++QRR+QK+IE Sbjct: 182 VAMTRQEAQTAFGNPMVYMEKFLENPRHVEIQVLADEFKNAVYLGERDCSMQRRHQKVIE 241 Query: 243 EAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPT 302 EAP+P + + E + + I Y GTFE + + +FYF+E+N R+QVEHP Sbjct: 242 EAPAPGIPARLIARVGERCAEACRRIGYRGAGTFEFLYE--NGEFYFIEMNTRVQVEHPV 299 Query: 303 TELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY 362 TELI ID+V+ QI++AAGE L F Q D+ + RG AIE R+NAED F S G +++ Sbjct: 300 TELITGIDIVQEQIRIAAGEKLRFKQRDI--QFRGHAIECRVNAEDPF-TFVPSPGTISW 356 Query: 363 YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 + P GPGVRVDS SG VPP+YDS++ K+I +G++RE AI+ AL++ + GIKT Sbjct: 357 WHPPGGPGVRVDSHAYSGYKVPPHYDSMIGKIITFGDTREQAIRRMRIALSETVVQGIKT 416 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQK 449 I L++ +MQD F EG S Y+ K Sbjct: 417 NIPLHQELMQDARFVEGGTSIHYLEHK 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: 560 Number of extensions: 21 Number of successful extensions: 5 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: 455 Length adjustment: 34 Effective length of query: 475 Effective length of database: 421 Effective search space: 199975 Effective search space used: 199975 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