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_3016 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3016 Length = 675 Score = 367 bits (941), Expect = e-106 Identities = 206/511 (40%), Positives = 303/511 (59%), Gaps = 21/511 (4%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F ++L+ANRGEIA RV + +G+ +AVYS+AD A H DEA +IG + DSYL Sbjct: 2 FKKILIANRGEIACRVAATAQRLGVKTVAVYSDADANAKHVAVCDEAVHIGGSAPKDSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 E II+AA+ AIHPGYGFLSEN +FA+A AG+ FIGP + ++ + K + K+ Sbjct: 62 RWERIIEAAKATGAQAIHPGYGFLSENEDFAQACAAAGLVFIGPPASAIKDMGLKAESKQ 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEAL--KLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMD 181 L AGVP PG G + D AL + A++IGYP+++KA++GGGG G+ VD + Sbjct: 122 LMEKAGVPLVPGYHG--SDQDPALLQREADRIGYPVLIKASAGGGGKGMRAVDKSEDFAA 179 Query: 182 VWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLI 241 E KR A +FG + +EKY PRHIE Q+ GD +GN V +ER+C++QRR+QK++ Sbjct: 180 ALESCKREAINSFGDDAVLVEKYVQRPRHIEIQVFGDMHGNCVYLFERDCSVQRRHQKVL 239 Query: 242 EEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDV-------SRDFYFLELNK 294 EEAP+P + R M E + K +NY GT E FYF+E+N Sbjct: 240 EEAPAPGMTPALRAQMGEAAVAAAKAVNYVGAGTVEFIVEQPGGYERPDQMKFYFMEMNT 299 Query: 295 RLQVEHPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFT 354 RLQVEHP TE I +DLV+ Q+++A+GE LP Q+DL R+ G AIE RI AE+ NNF Sbjct: 300 RLQVEHPVTEAITGLDLVEWQLRVASGEPLPLQQQDL--RITGHAIEARICAENPDNNFL 357 Query: 355 GSSGFVTYYREP-----TGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGI 409 ++G + Y P +RVDSG+ G + P+YDS+V+KLIV+G++RE A+ Sbjct: 358 PATGALNVYALPECVTFERGAIRVDSGVRQGDAISPFYDSMVAKLIVHGDTREQALARLD 417 Query: 410 RALADYKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAA 469 ALA I G+ T ++ + + + F + K T+ I + +Q V + +E + A AA Sbjct: 418 DALAQTHIVGLATNVQFLRRVAKTDAFAQAKLDTALIPR--EQAVLFHQEPVGLPLAAAA 475 Query: 470 EIQSRGLLRTSSTDNKGKAQSKSGWKTYGII 500 + ++ LL+ +++ + G+ T+G++ Sbjct: 476 AV-AQTLLKERASEGVDPFSRRDGFHTHGVV 505 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: 785 Number of extensions: 39 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: 675 Length adjustment: 37 Effective length of query: 472 Effective length of database: 638 Effective search space: 301136 Effective search space used: 301136 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: 53 (25.0 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