Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate HSERO_RS22345 HSERO_RS22345 urea carboxylase
Query= reanno::SB2B:6937189 (673 letters) >FitnessBrowser__HerbieS:HSERO_RS22345 Length = 1207 Score = 380 bits (976), Expect = e-109 Identities = 226/528 (42%), Positives = 311/528 (58%), Gaps = 23/528 (4%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 MF+ LLIANRG IACR++RT R + + V VYS+AD + HV AD + LGE A +Y Sbjct: 1 MFDHLLIANRGAIACRILRTLRTLDVTGVCVYSEADLGSLHVLQADRAISLGEGPAAQTY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L + I+ A+ GA+AIHPGYGFLSENAAFA ACEA+GIAFVGP + G K A+ Sbjct: 61 LAVDKILAAARDSGAQAIHPGYGFLSENAAFAEACEAAGIAFVGPTPAQLRIFGLKHTAR 120 Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180 + + GVP++ G + D L A A ++GYP+++K+ GGGG GMR+ S++EL A Sbjct: 121 ALAREQGVPMLEGTDLLESIDDALAA-ASRVGYPVMLKSTAGGGGIGMRVCRSDAELADA 179 Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240 DS RR ++F + + +E+Y+ + RH+EVQVF D +G + L RDCS+QRR+QKV+E Sbjct: 180 FDSVRRLGQNNFSDAGVFIEKYIERARHLEVQVFGDGRGEVIALGVRDCSVQRRNQKVLE 239 Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLD-VDMSFFFMEMNTRLQVEHPV 299 E PAP LPD + + + AA+ AKA++YR AGTVEF+ D + F+F+E+NTRLQVEH V Sbjct: 240 ETPAPNLPDGMAEALCAAAIKLAKAVNYRSAGTVEFVYDSLAGQFYFLEVNTRLQVEHGV 299 Query: 300 TEMVTGQDLVKWQLLVAAGAQLPLEQ--HEIQIHGHAFEVRIYAEDPNNEFLPASGKLTF 357 TE V G DLV+W + +AAG PL Q +Q GHA + R+YAEDP +F P G LT Sbjct: 300 TEQVWGVDLVRWMIELAAGDLPPLAQLAAGLQPRGHAIQARLYAEDPGRQFQPCPGLLTA 359 Query: 358 LR-EPEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGL 416 + P + +RID+ V I+ Y+DPMIAKLI W +R A L AL + G+ Sbjct: 360 VDFPPVDGQALRIDTWVEAGCEIAPYFDPMIAKLISWQPTREAARLALDAALRATLLYGV 419 Query: 417 KHNIEFLSNIAEHPAFAQANFSTDFIGRYGDALIGDSRDEADTAFVLAVLTQLRLRE--- 473 + N +L I FA G+ + ADT VLA TQ +++ Sbjct: 420 ETNQHYLRQILADVPFAS--------GQPWTRCLEQLVYRADTVEVLAPGTQTTVQDHPG 471 Query: 474 AVSQDVAGHDPFSPWSSLKGFRLSSPRRHSVTLLDDAHQSRSAELTES 521 + G P P + RL + LL +A ++ E+T S Sbjct: 472 RIGYWAVGVPPSGPMDE-RALRLGN------RLLGNAEEAAGLEVTMS 512 Score = 50.8 bits (120), Expect = 4e-10 Identities = 32/97 (32%), Positives = 54/97 (55%), Gaps = 4/97 (4%) Query: 568 FLSSGSYHFR-EVLGQVLEETASSED---KLKAPMNGTVVTHLVAAGDKVSAGQGLLVME 623 +++SG ++ E + +E A +D + AP+ G + V+ G +V+ G+ L+++E Sbjct: 1104 WIASGQANYESEESSAIAQEAAPLQDGQMAVDAPIAGNLWQVKVSPGQRVAQGELLMILE 1163 Query: 624 AMKMEYTIEAPFDGVVSEFFFAPGELVSDGTLLLALE 660 +MKME I AP GVV+E PG V G +L +E Sbjct: 1164 SMKMEIHIAAPAAGVVAEVRVQPGSPVRAGQCVLVME 1200 Score = 27.7 bits (60), Expect = 0.003 Identities = 17/43 (39%), Positives = 21/43 (48%) Query: 586 ETASSEDKLKAPMNGTVVTHLVAAGDKVSAGQGLLVMEAMKME 628 E+ E + AP G V V G V AGQ +LVME + E Sbjct: 1163 ESMKMEIHIAAPAAGVVAEVRVQPGSPVRAGQCVLVMEDTEEE 1205 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: 1746 Number of extensions: 83 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 673 Length of database: 1207 Length adjustment: 43 Effective length of query: 630 Effective length of database: 1164 Effective search space: 733320 Effective search space used: 733320 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