Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_028311442.1 H566_RS0110680 ATP-grasp domain-containing protein
Query= reanno::Smeli:SM_b21124 (662 letters) >NCBI__GCF_000482785.1:WP_028311442.1 Length = 1295 Score = 430 bits (1106), Expect = e-124 Identities = 233/442 (52%), Positives = 304/442 (68%), Gaps = 7/442 (1%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 MF K+LIANRG IACR+IRT RR+G+++VAV+SDAD + HV+ ADEA+R+G APA+ESY Sbjct: 1 MFDKVLIANRGAIACRVIRTLRRMGVKSVAVFSDADRHSRHVSEADEAVRLGPAPASESY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L I+ AA+ GAQAIHPGYGFLSENADFAEA A AG+ F+GP PA +R GLK A+ Sbjct: 61 LRVDLILDAAKRTGAQAIHPGYGFLSENADFAEACAAAGIAFIGPTPAQMRDFGLKHTAR 120 Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 AL +GVP+ PG + A+ AR IGYPV++K+ AGGGG GM+ V A Sbjct: 121 ALALAAGVPLSPGSDLLPDLDTARAEAAR-IGYPVMLKSTAGGGGIGMQLVRDPAALDAA 179 Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 + +R A SAF G + LE+Y+ + RHIE+Q+FGD GN+V L ERDCSLQRR+QKV+E Sbjct: 180 YASVQRLATSAFKSGGMFLEKYIEQARHIEVQIFGDGRGNVVALGERDCSLQRRNQKVVE 239 Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300 EAPAPG++AE R + A ++I Y AGTVEF+ DV +G FYF+E+NTRLQV Sbjct: 240 EAPAPGLSAEQRARLHRTAADLGRSISYQSAGTVEFVYDVPSG----EFYFLEVNTRLQV 295 Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360 EH VTE ITGIDLVEW ++ A+GE L + S G + +ARLYAEDPAR F P++G L Sbjct: 296 EHGVTEQITGIDLVEWMVKQAAGE-LDLAGFEPSFAGHSIQARLYAEDPARNFQPSSGLL 354 Query: 361 TELSFPEGTSRVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGGTV 420 T++++ + +R+++ V +G + P YDP+IAK+IV +R AA+ L DAL RIGG Sbjct: 355 TDVAWAD-AARIETWVERGSIVPPNYDPMIAKIIVTAADREAAIAALGDALAGTRIGGIE 413 Query: 421 TNRDFLIRLTEEHDFRSGHPDT 442 TN +L +T F G T Sbjct: 414 TNLGYLRAITASDTFARGEQTT 435 Score = 43.9 bits (102), Expect = 5e-08 Identities = 25/66 (37%), Positives = 38/66 (57%) Query: 591 LVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHVAEGAQVSEG 650 + +P+ G V + V G V+ G LVV+E+MKME ++A G++ ++ EGA V G Sbjct: 1228 IASPVSGSVWKLAVEPGQRVSAGDTLVVVESMKMEFPVAAPVGGSVTHLLCHEGAPVQAG 1287 Query: 651 TVLVTL 656 LV L Sbjct: 1288 QNLVGL 1293 Lambda K H 0.319 0.135 0.394 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: 2195 Number of extensions: 125 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: 662 Length of database: 1295 Length adjustment: 43 Effective length of query: 619 Effective length of database: 1252 Effective search space: 774988 Effective search space used: 774988 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 (21.8 bits) S2: 57 (26.6 bits)
This GapMind analysis is from Sep 24 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