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 Ac3H11_4028 Biotin carboxylase of acetyl-CoA carboxylase (EC 6.3.4.14)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4028 Length = 449 Score = 384 bits (986), Expect = e-111 Identities = 207/450 (46%), Positives = 292/450 (64%), Gaps = 6/450 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F ++LVANRGEIA R+ +A E+G+ A+ VYSEAD+ A + K A+EA IG AP+ SYL Sbjct: 2 FKKILVANRGEIALRIQRACSELGIKAVMVYSEADRDAKYVKLAEEAVCIGPAPSPLSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 N+ II AAE +AIHPGYGFLSENA+FAE VEK+G FIGP+ E +R + DK+ K+ Sbjct: 62 NMPAIISAAEVTDAEAIHPGYGFLSENADFAERVEKSGFQFIGPTPESIRIMGDKVSAKQ 121 Query: 124 LANMAGVPTAPGSDGPVTSID-EALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDV 182 AGVP PGS+G + + ++A+ +GYP+++KAA GGGG G+ V + L++ Sbjct: 122 AMIRAGVPCVPGSEGELPDDPVQIRRIAKAVGYPVIIKAAGGGGGRGMRVVHTEAALVNA 181 Query: 183 WERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIE 242 + K A AFG +++EK+ NPRHIE Q++ DK+ N V ER+C++QRR+QK+IE Sbjct: 182 VQMTKAEAGAAFGNPAVYMEKFLQNPRHIEIQILADKHRNAVYLGERDCSMQRRHQKVIE 241 Query: 243 EAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPT 302 EAP+P + + E + E + K I Y GTFE + + +FYF+E+N R+QVEHP Sbjct: 242 EAPAPGIPRKLIEKIGERCVAACKKIGYRGAGTFEFLYE--NGEFYFIEMNTRVQVEHPV 299 Query: 303 TELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY 362 TE I +D+VK QI +AAGE LPF+Q + +RG AIE R+NAED F S G +T Sbjct: 300 TEWITGVDIVKTQIMVAAGEKLPFTQRQI--EIRGHAIECRVNAEDPY-KFVPSPGRITT 356 Query: 363 YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 + P GPGVRVDS + +VPP YDS++ K+IV+G++RE A+ AL++ I GI T Sbjct: 357 WHPPGGPGVRVDSHAYTNYFVPPNYDSMIGKIIVHGDTREQALARMRTALSETVIEGINT 416 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQ 452 + L++ +M D F G + Y+ + Q Sbjct: 417 NVPLHRELMVDAKFMAGGTNIHYLEEWLSQ 446 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: 581 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: 449 Length adjustment: 34 Effective length of query: 475 Effective length of database: 415 Effective search space: 197125 Effective search space used: 197125 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