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_111392413.1 CLV31_RS08220 acetyl-CoA carboxylase biotin carboxylase subunit
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_003253485.1:WP_111392413.1 Length = 498 Score = 406 bits (1044), Expect = e-118 Identities = 215/473 (45%), Positives = 308/473 (65%), Gaps = 6/473 (1%) Query: 1 MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60 M S++LVANRGEIA R+++ +EMG++ +AVYSEAD+ + H K ADEA +G P+ Sbjct: 1 MAKISKLLVANRGEIALRIMRTAREMGISTVAVYSEADRLSPHVKLADEAICLGPPPSNQ 60 Query: 61 SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120 SYL + II VDAIHPGYGFLSENAEFA+ V +AG+ F+GPS E + + KL Sbjct: 61 SYLLGDKIIKTCLDLGVDAIHPGYGFLSENAEFAKKVTQAGLIFVGPSPESIEVMGSKLA 120 Query: 121 GKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLM 180 K+ +P PG++ ++ I A A +IGYPI++KA++GGGG G+ V+++++ Sbjct: 121 AKQAVAKYDIPLVPGTEEAISDIAAAKVKAAEIGYPILIKASAGGGGKGMRIVESEEEFE 180 Query: 181 DVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKL 240 + +R A AFG +FIEK+ +PRHIE Q++GD+ GN V +EREC+IQRR+QK+ Sbjct: 181 EQMQRAVSEAQSAFGDGAVFIEKFITSPRHIEIQVLGDQQGNTVYLFERECSIQRRHQKV 240 Query: 241 IEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEH 300 IEEAPS + E R++M E + K NY+ GT E D +FYFLE+N RLQVEH Sbjct: 241 IEEAPSAVVSPEMRKAMGEAAVGVAKACNYYGAGTVEFIVDD-QLNFYFLEMNTRLQVEH 299 Query: 301 PTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFV 360 P TE+I DLV+ QI +A G LPF+QEDL ++ G A+E R+ AED NNF G + Sbjct: 300 PVTEMITGKDLVREQILIAEGNPLPFAQEDL--QINGHAVEIRVYAEDPKNNFLPDIGKL 357 Query: 361 TYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGI 420 YR P GPG+RVD G E G +P YYD +++KLI +G +RE AI I A+ Y+I GI Sbjct: 358 VTYRRPQGPGIRVDDGFEEGMDIPIYYDPMIAKLITHGSNREEAINRMIGAINAYRITGI 417 Query: 421 KTTIELYKWIMQDPDFQEGKFSTSYISQK-TDQFVKYL--REQEEIKAAIAAE 470 +TT++ ++ +Q F G+F T ++ + T + ++++ E++E+ AA+A E Sbjct: 418 QTTLDFCRFALQHEAFVSGQFDTKFVERYFTPEKLEHVFSEEEKELLAALAVE 470 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: 586 Number of extensions: 26 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: 498 Length adjustment: 34 Effective length of query: 475 Effective length of database: 464 Effective search space: 220400 Effective search space used: 220400 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: 52 (24.6 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