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 Echvi_3962 Echvi_3962 Acetyl/propionyl-CoA carboxylase, alpha subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Cola:Echvi_3962 Length = 499 Score = 432 bits (1110), Expect = e-125 Identities = 229/499 (45%), Positives = 317/499 (63%), Gaps = 8/499 (1%) Query: 1 MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60 MP ++LVANRGEIA R+++ I+EMG+ ++AVYSE DK A H YADE+Y +G AP+ Sbjct: 1 MPKIRKILVANRGEIALRIMRTIREMGLKSVAVYSEVDKNAPHVLYADESYCLGPAPSHK 60 Query: 61 SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120 SYL E II+A + DAIHPGYGFLSEN FA+ V AG+ FIGPS E + + DKL Sbjct: 61 SYLLGERIIEACQALGADAIHPGYGFLSENTAFAKKVADAGLIFIGPSPESIEIMGDKLA 120 Query: 121 GKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLM 180 K+ + +P PG+D + I EA K A +IGYPI++KA++GGGG G+ V ++ + Sbjct: 121 AKKAVSHYDIPMVPGTDHAILDIQEAKKTAVEIGYPILIKASAGGGGKGMRIVQDEGEFE 180 Query: 181 DVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKL 240 + +R A AFG +FIEKY +PRHIE Q++ D++GNY+ +EREC++QRR+QK+ Sbjct: 181 EQMKRAVSEAQSAFGDGAVFIEKYITSPRHIEIQILADQHGNYLHLFERECSVQRRHQKV 240 Query: 241 IEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEH 300 IEEAPS + E R++M + I K Y+ GT E D + +FYFLE+N RLQVEH Sbjct: 241 IEEAPSAVVNQEMRKAMGQAAIDVAKACQYYGAGTVE-FIVDEALNFYFLEMNTRLQVEH 299 Query: 301 PTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFV 360 P TE+I DLV+ QI +A G+ L F+Q+DL + G AIE R+ AED NNF G + Sbjct: 300 PVTEMITGKDLVREQIFIAEGQALSFAQDDLT--ILGHAIETRVYAEDPTNNFLPDIGKL 357 Query: 361 TYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGI 420 YR P GPG+RVD G G +P YYD +++KL+ + E R AIQ +RA+ DY I GI Sbjct: 358 ATYRLPQGPGIRVDDGFREGMEIPIYYDPMIAKLVTFEEDRPKAIQKMVRAIDDYHITGI 417 Query: 421 KTTIELYKWIMQDPDFQEGKFSTSYISQ---KTDQFVKYLREQEEIKAAIAAEIQSRGLL 477 TT+ +++M P FQ G+F T ++ + + + E+EEI A IAA + Sbjct: 418 STTLSFARFVMLHPAFQSGEFDTKFVEKHFAPSKLAENFSEEEEEILATIAAYLLPNA-- 475 Query: 478 RTSSTDNKGKAQSKSGWKT 496 + ST+ G+ Q+ S WKT Sbjct: 476 KQPSTNVNGQDQNNSKWKT 494 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: 603 Number of extensions: 34 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: 499 Length adjustment: 34 Effective length of query: 475 Effective length of database: 465 Effective search space: 220875 Effective search space used: 220875 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 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