Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate GFF2304 Psest_2351 urea carboxylase
Query= SwissProt::Q5LUF3 (681 letters) >FitnessBrowser__psRCH2:GFF2304 Length = 1199 Score = 395 bits (1015), Expect = e-114 Identities = 233/557 (41%), Positives = 324/557 (58%), Gaps = 51/557 (9%) Query: 1 MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60 MF+K+LIANRG IACR+++T R + + +VA+YS+AD +LH+Q ADEA +G PA Q+Y Sbjct: 1 MFDKLLIANRGAIACRILRTLRGLDVKSVAVYSEADAASLHIQQADEAHSLGEGPAAQTY 60 Query: 61 IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120 +V++K++ R TGA A+HPGYGFLSEN+ FAEA EA G+ FVGP + G K T++ Sbjct: 61 LVVEKILRIARETGASAIHPGYGFLSENAAFAEACEAAGIAFVGPTPEQLRMFGLKHTAR 120 Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180 +A++ V + G L++ +A+ + Q+GYPVM+K++AGGGG GMR+ + E E Sbjct: 121 ALAKQRGVPMLEG-TELLDSLADALGAAEQVGYPVMLKSTAGGGGIGMRVCRSAAELAEA 179 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240 F + K N+F D +FIEK++ + RH+E+QV D G I LG R+CS+QRRNQKV+E Sbjct: 180 FDAVKRLGQNNFSDAGVFIEKYIQRARHLEVQVFGDGRGEVIALGVRDCSVQRRNQKVLE 239 Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQ-KNFYFLEMNTRLQVEHPV 299 E P+P L A+ E AV LAKAV Y SAGTVEF+ D + + FYFLE+NTRLQVEH V Sbjct: 240 ETPAPNLPAGMAEALCEAAVKLAKAVSYRSAGTVEFVYDAEAEQFYFLEVNTRLQVEHGV 299 Query: 300 TELITGVDLVEQMIRVAAGE--PLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTR 357 TE + GVDLV MI +AAG+ PL +K +G +I+ RLYAEDP R F PS G LT Sbjct: 300 TEQVWGVDLVRWMIELAAGDLPPLVELARALKSSGHSIQARLYAEDPGRDFQPSPGLLTV 359 Query: 358 YRPPAETAAGPLLVNGKWQGDAPSGEA-AVRNDTGVYEGGEISMYYDPMIAKLCTWAPTR 416 D P G+ A+R DT V G EI Y+DPM+AKL TWAP R Sbjct: 360 V-------------------DFPKGDGKALRIDTWVEAGCEIPPYFDPMVAKLITWAPDR 400 Query: 417 AAAIEAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISG--------------------DM 456 +A A+ ALD + G+ N +L ++ + F G Sbjct: 401 ESARAALDTALDETLLYGVESNRAYLRQILGYAPFAEGRPWTRCLEGLTYRATTFEVISA 460 Query: 457 TTAFIAEEYPE--GFEGVNLPET---DLRRVAAAAAAMHRVAEIRRTRVSGRMDNHERRV 511 T +++P G+ V +P + D R + A + + ++ M R Sbjct: 461 GTQTTVQDFPGRLGYWAVGVPPSGPMDNRALRLGNALLGNPEDAAGLEIT--MSGPILRF 518 Query: 512 GTEWVVTLQGADFPVTI 528 T+ VV + GA+ PV + Sbjct: 519 NTDAVVAITGAEIPVKL 535 Score = 35.4 bits (80), Expect = 2e-05 Identities = 20/61 (32%), Positives = 31/61 (50%) Query: 621 GLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEKKGVVAKINASAGNSLAVDDVIMEF 680 G + +V V G V+ G L +E+MKME L A GVV ++ A G+ + ++ Sbjct: 1137 GNLWQVSVAEGARVEAGDVLVILESMKMEIPLTAPVAGVVKEVRAQPGSPVRAGQRVVVI 1196 Query: 681 E 681 E Sbjct: 1197 E 1197 Lambda K H 0.317 0.134 0.387 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: 1910 Number of extensions: 98 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 681 Length of database: 1199 Length adjustment: 43 Effective length of query: 638 Effective length of database: 1156 Effective search space: 737528 Effective search space used: 737528 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