Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate AO353_28810 AO353_28810 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::PS:Dsui_0516 (663 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28810 Length = 457 Score = 399 bits (1026), Expect = e-115 Identities = 203/440 (46%), Positives = 299/440 (67%), Gaps = 5/440 (1%) Query: 4 KILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYLVA 63 K+L+ANRGEIA R+I+ A+++GI TVA SEAD D+ MADE +GPA + +SYL Sbjct: 7 KLLVANRGEIAVRIIRAAKELGIPTVAACSEADVDSQAARMADEVHILGPARADKSYLNV 66 Query: 64 DKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKKLA 123 + ++ A K TGA AVHPGYGFLSENA+F+ + G F+GP +I +MGDK E+++ A Sbjct: 67 EALLGALKATGANAVHPGYGFLSENADFAEAVLAAGAIFVGPSPETIRRMGDKAEARRTA 126 Query: 124 IEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGFSS 183 A V +PG + ++A++ A+ +G+P++IKASAGGGG+G+R+A N + E F Sbjct: 127 QAAGVPVVPGSPGELFDVESALKAAESVGFPLLIKASAGGGGRGIRLAENAEQLSEEFPR 186 Query: 184 CVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEEAP 243 EA+ +FG+ V++E+++ RHIE+QVLGD + V+L ER+CS+QRR QK+ EEAP Sbjct: 187 SQREAQAAFGNGAVYLERFISRARHIEVQVLGDGQ-HAVHLFERECSLQRRRQKIFEEAP 245 Query: 244 SPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVTEL 303 SP + + R+ + AV L ++ Y+ AGT+E++ AT EF+F+EMNTR+QVEHPV+EL Sbjct: 246 SPVLSQQQRETLCASAVRLTESLGYKGAGTLEYLYDDATGEFFFIEMNTRIQVEHPVSEL 305 Query: 304 ITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQPPA 363 ITG+DLV+ M+R+A GE L Q+D+++NG A++ R+NAEDP R F PS G + + P Sbjct: 306 ITGIDLVQAMLRIAGGEPLGFKQSDIRLNGAALQMRLNAEDPARDFFPSPGLVEELIWP- 364 Query: 364 EVDGQ-VRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISSNI 422 +G+ +RVDT +Y G + YYDS++AKLIVHGA R +A+A R A+ + G+++ + Sbjct: 365 --NGEGIRVDTHLYQGYRVPPYYDSLLAKLIVHGADRAEALALARMAVAHTTLTGMANTL 422 Query: 423 PFQAALMQHARFQSGIFDTG 442 L++ S F TG Sbjct: 423 ALHGELLEQPWLHSADFHTG 442 Lambda K H 0.319 0.135 0.391 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: 737 Number of extensions: 28 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: 663 Length of database: 457 Length adjustment: 36 Effective length of query: 627 Effective length of database: 421 Effective search space: 263967 Effective search space used: 263967 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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