Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate Pf6N2E2_2411 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= BRENDA::Q9I299 (655 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2411 Length = 656 Score = 563 bits (1452), Expect = e-165 Identities = 321/659 (48%), Positives = 421/659 (63%), Gaps = 22/659 (3%) Query: 7 SIQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSY 66 + ++L+ANRGEIACR+ R+A+ALG +VAV S+ D A HV AD AV +G A SY Sbjct: 3 AFSKILIANRGEIACRIQRTAQALGYRTVAVFSEADADALHVRMADEAVLIGPAAAQQSY 62 Query: 67 LRGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAK 126 L I+ AA GA AIHPGYGFLSENA FA+ACE A ++F+GP AID MGSK AK Sbjct: 63 LNPSAILDAARRCGADAIHPGYGFLSENAGFAKACEAADIVFIGPSPEAIDLMGSKRRAK 122 Query: 127 ALMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEA 186 M EAGVP + GY G AQD +T +REAGRIGYP+++KA+AGGGG+GM++V+R +L E Sbjct: 123 IAMIEAGVPCIAGYQGAAQDDDTLQREAGRIGYPLMIKASAGGGGRGMRLVQRAEDLLEQ 182 Query: 187 LSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVE 246 L A+ EA FG +++E+ L+ PRHVE+Q+F D HG ++L ERDCSIQRRHQKV+E Sbjct: 183 LRGARSEALHGFGSDELILEQALIDPRHVEVQIFGDHHGQLIHLGERDCSIQRRHQKVIE 242 Query: 247 EAPAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVT 306 EAP P + +LRRAMG+AA++AA+A+ YVGAGTVEFLL G+F+F+EMNTRLQVEHPVT Sbjct: 243 EAPCPVMTTDLRRAMGDAALKAARAVNYVGAGTVEFLLAADGRFYFLEMNTRLQVEHPVT 302 Query: 307 EAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYRE 366 E ITGLDLVAWQ+ VA G +LPL QEQV L+GHA++VRLYAEDP DFLP +GRL+ + E Sbjct: 303 ELITGLDLVAWQLDVAAGRSLPLRQEQVTLSGHAMQVRLYAEDPAADFLPQTGRLIGW-E 361 Query: 367 AAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNL 426 + G R+D G+ EG ++PFYD ML KLI G TREEAR++LL + + + G+++N Sbjct: 362 PPSQDGVRIDHGLLEGQAITPFYDSMLGKLIVHGATREEARRKLLRAVEDCVLLGVQSNQ 421 Query: 427 AFLRRILGHPAFAAAELDTGFIARHQDD------LLPAPQAL---PEHFWQAAAEAWLQS 477 L +L HP F + GFI +H D L P+ + L F+QA+ Q Sbjct: 422 RLLTGLLAHPRFIDGDFGNGFIGQHFADHAALRPLEPSAEQLAIATAAFYQASQARHAQG 481 Query: 478 EPGHRRDDDPHSPWSRNDG---WRSALARESDLMLRCRDERRCVRLRHASPSQYRLDGDD 534 G R + G W +L E+D R R + LR + + G Sbjct: 482 LGGWRNSIGVVLHYRIGVGEHDWTLSLVAEADGTFNIRSAGRLIELRLLDAAPH---GAT 538 Query: 535 LVSRVDGVTRRSAALRRGRQLFLEW--EGELLAIEAVDPIAEAEAAHAHQGGLSAPMNGS 592 LV +DG+ RR A G L+L G L + PIA + A G L APM+G+ Sbjct: 539 LV--IDGIRRRHAWRLDGNDLWLFTCPGGLHLQDRTLAPIAAKTS--ASDGTLKAPMDGA 594 Query: 593 IVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGTPLVELD 651 IV + V G TV G L+VLEAMKMEH ++A GVV L + G+ V++ L+ ++ Sbjct: 595 IVELRVREGSTVHQGQLLMVLEAMKMEHPLKAGVDGVVTHLQVARGDQVKKRQVLLRVE 653 Lambda K H 0.319 0.135 0.397 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: 1066 Number of extensions: 47 Number of successful extensions: 4 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: 655 Length of database: 656 Length adjustment: 38 Effective length of query: 617 Effective length of database: 618 Effective search space: 381306 Effective search space used: 381306 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: 54 (25.4 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