Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF2304 Psest_2351 urea carboxylase
Query= reanno::SB2B:6937189 (673 letters) >FitnessBrowser__psRCH2:GFF2304 Length = 1199 Score = 392 bits (1007), Expect = e-113 Identities = 208/438 (47%), Positives = 291/438 (66%), Gaps = 5/438 (1%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 MF+KLLIANRG IACR++RT R + +K+VAVYS+AD + H+ ADE+ LGE A +Y Sbjct: 1 MFDKLLIANRGAIACRILRTLRGLDVKSVAVYSEADAASLHIQQADEAHSLGEGPAAQTY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L E I+ IA++ GA AIHPGYGFLSENAAFA ACEA+GIAFVGP + + G K A+ Sbjct: 61 LVVEKILRIARETGASAIHPGYGFLSENAAFAEACEAAGIAFVGPTPEQLRMFGLKHTAR 120 Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180 + ++ GVP++ G D S A L A+++GYP+++K+ GGGG GMR+ S +EL A Sbjct: 121 ALAKQRGVPMLEGTELLD-SLADALGAAEQVGYPVMLKSTAGGGGIGMRVCRSAAELAEA 179 Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240 D+ +R ++F + + +E+Y+++ RH+EVQVF D +G + L RDCS+QRR+QKV+E Sbjct: 180 FDAVKRLGQNNFSDAGVFIEKYIQRARHLEVQVFGDGRGEVIALGVRDCSVQRRNQKVLE 239 Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDM-SFFFMEMNTRLQVEHPV 299 E PAP LP + + + EAAV AKA+ YR AGTVEF+ D + F+F+E+NTRLQVEH V Sbjct: 240 ETPAPNLPAGMAEALCEAAVKLAKAVSYRSAGTVEFVYDAEAEQFYFLEVNTRLQVEHGV 299 Query: 300 TEMVTGQDLVKWQLLVAAGAQLPLEQ--HEIQIHGHAFEVRIYAEDPNNEFLPASGKLTF 357 TE V G DLV+W + +AAG PL + ++ GH+ + R+YAEDP +F P+ G LT Sbjct: 300 TEQVWGVDLVRWMIELAAGDLPPLVELARALKSSGHSIQARLYAEDPGRDFQPSPGLLTV 359 Query: 358 LREPE-PSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGL 416 + P+ + +RID+ V I Y+DPM+AKLI W R A A L AL + + G+ Sbjct: 360 VDFPKGDGKALRIDTWVEAGCEIPPYFDPMVAKLITWAPDRESARAALDTALDETLLYGV 419 Query: 417 KHNIEFLSNIAEHPAFAQ 434 + N +L I + FA+ Sbjct: 420 ESNRAYLRQILGYAPFAE 437 Score = 48.1 bits (113), Expect = 2e-09 Identities = 33/99 (33%), Positives = 52/99 (52%), Gaps = 4/99 (4%) Query: 568 FLSSGSYHFR--EVLGQVLEET--ASSEDKLKAPMNGTVVTHLVAAGDKVSAGQGLLVME 623 +++SG HF EV + E+ S +++ + G + VA G +V AG L+++E Sbjct: 1101 WIASGQAHFESEEVAADLGEDAPLGSGLHGIESHIAGNLWQVSVAEGARVEAGDVLVILE 1160 Query: 624 AMKMEYTIEAPFDGVVSEFFFAPGELVSDGTLLLALEMA 662 +MKME + AP GVV E PG V G ++ +E A Sbjct: 1161 SMKMEIPLTAPVAGVVKEVRAQPGSPVRAGQRVVVIEEA 1199 Lambda K H 0.317 0.134 0.380 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: 1777 Number of extensions: 85 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 673 Length of database: 1199 Length adjustment: 43 Effective length of query: 630 Effective length of database: 1156 Effective search space: 728280 Effective search space used: 728280 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