Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate CCNA_01905 CCNA_01905 urea carboxylase
Query= reanno::Dino:3607308 (681 letters) >FitnessBrowser__Caulo:CCNA_01905 Length = 1207 Score = 403 bits (1035), Expect = e-116 Identities = 223/459 (48%), Positives = 296/459 (64%), Gaps = 24/459 (5%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60 MF K+LIANRG IACR+I+T R MG+++VA++SDAD +LHV MADEAV +GP+PA +SY Sbjct: 1 MFDKVLIANRGAIACRIIRTLRAMGVKSVAVFSDADAGSLHVSMADEAVRLGPAPAAESY 60 Query: 61 IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120 + D V+ A + TGA+A+HPGYGFLSE+ FA+A E GV FIGP A+ I A G K T++ Sbjct: 61 LRADLVLAAAQATGAQAIHPGYGFLSESAAFAQACEDAGVTFIGPSADNIRAFGLKHTAR 120 Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180 +AQ V PG L+ D A+ + IG+PV++KA+AGGGG GMR+ + E Sbjct: 121 DLAQAHGVPLAPG-TDLLTDPAAALAAAQRIGFPVILKATAGGGGIGMRVCESAEAVEEA 179 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240 F + + A +F D +F+E++V + RHIE+QV D G LGER+CS+QRRNQKVVE Sbjct: 180 FAAVRRLATGNFSDGGVFLERYVHKARHIEVQVFGDGAGRVAALGERDCSLQRRNQKVVE 239 Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDR-NFYFLEMNTRLQVEHPV 299 E P+P L ATR A+ + + LA+A Y SAGTVEF+ D DR +F+FLE+NTRLQVEH V Sbjct: 240 ETPAPGLPAATRTALLDAAVRLAKAANYRSAGTVEFLYDADRDDFFFLEVNTRLQVEHGV 299 Query: 300 TELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYR 359 TE +TGVDLVE M+R AAG+ + G AI+ RLYAEDP +++ PS G LT Sbjct: 300 TEQVTGVDLVEWMVRGAAGDFSFLDTPPPAPRGAAIQVRLYAEDPAQDYRPSAGVLT--- 356 Query: 360 PPVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAA 419 EVA P VR D V +G E+S +YDPM+AKL RPAA Sbjct: 357 ---EVAF----------------PEGVRADGWVVDGTEVSAFYDPMLAKLIVIAEHRPAA 397 Query: 420 IEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTT 458 + A++ ALD + GI NL ++ V F+ GE++T Sbjct: 398 VAALQAALDATRLAGIETNLDWLRTVTRSQPFVSGEVST 436 Lambda K H 0.318 0.134 0.392 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: 2084 Number of extensions: 102 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: 681 Length of database: 1207 Length adjustment: 43 Effective length of query: 638 Effective length of database: 1164 Effective search space: 742632 Effective search space used: 742632 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 (21.7 bits) S2: 56 (26.2 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