Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate WP_005458894.1 SACCYDRAFT_RS19840 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= BRENDA::Q9I299 (655 letters) >NCBI__GCF_000244975.1:WP_005458894.1 Length = 660 Score = 580 bits (1495), Expect = e-170 Identities = 332/654 (50%), Positives = 425/654 (64%), Gaps = 25/654 (3%) Query: 11 LLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYLRGD 70 +LVANRGEIA RV+ + R LGI SVAV+SD D ARHVAEAD+A +G A A SYL Sbjct: 5 VLVANRGEIAVRVIATLRRLGIRSVAVYSDADADARHVAEADVARRVGPADAARSYLSVP 64 Query: 71 RIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKALME 130 I+AAA+ +GAQA+HPGYGFLSENA FA+ACE+AG++F+GPP AAIDAMG K AK + Sbjct: 65 DIVAAAVETGAQAVHPGYGFLSENAAFAKACEDAGIVFVGPPVAAIDAMGDKIRAKETVS 124 Query: 131 EAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEALSSA 190 AGVP+VPG + + D+++ A R+GYPVLLK +AGGGGKGM++V AEL A+ SA Sbjct: 125 AAGVPVVPGAN-DVSDVDSVAAAAERVGYPVLLKPSAGGGGKGMRLVREPAELPAAVESA 183 Query: 191 QREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEEAPA 250 QREA+ AFGD R+LVE+++ PRH+EIQV ADRHG ++L ER+CS+QRRHQK+VEEAP+ Sbjct: 184 QREARGAFGDDRLLVERFVADPRHIEIQVLADRHGTVVHLGERECSLQRRHQKIVEEAPS 243 Query: 251 PGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERG--QFFFMEMNTRLQVEHPVTEA 308 L A+ R MG+AAV AA+++GYVGAGTVEF++ +FFF+EMNTRLQVEHPVTE Sbjct: 244 TLLDADTRARMGKAAVEAARSVGYVGAGTVEFIVSSSAPDEFFFLEMNTRLQVEHPVTEL 303 Query: 309 ITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREAA 368 +TGLDLV WQ+RVA GE L TQ+ V L+GHA+E R+YAEDP DF+P G ++ E A Sbjct: 304 VTGLDLVEWQLRVAAGEPLTFTQDDVRLDGHAVEARVYAEDPARDFVPTGGTVLGLHE-A 362 Query: 369 AGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLAF 428 +GP RVDSG+R+G V+ YDPMLAK+IAWG R A RL LA+T+V G+ TN+ F Sbjct: 363 SGPHVRVDSGLRQGTAVASHYDPMLAKVIAWGPDRTSALHRLDRALADTAVLGVPTNVPF 422 Query: 429 LRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEAWLQSEPGHRRDDDPH 488 LR +L HP A LDTG + R L P + E F AA + L P D Sbjct: 423 LRTLLRHPDVVAGRLDTGLVERELSVLTADPDPV-EFFVAAALDRVLSLWPTGPVID--- 478 Query: 489 SPWSRNDGWRSALARESDLMLRCRDERRCVRLRHASPSQYRL--------------DGDD 534 PW GWR + LR VR+ P+Q R+ +G D Sbjct: 479 -PWDVPSGWRLGGNAGVTMRLRVGAAEALVRV-EGLPAQARVVVDGAEAVSASAAREGAD 536 Query: 535 LVSRVDGVTRR-SAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGGLSAPMNGSI 593 LV RV G RR A ++ EG ++A+ + + A G +++PM G++ Sbjct: 537 LVVRVAGEYRRYRRAEACDGAVWYAREGRVVAVSERPNLLASHAESVAAGPVTSPMPGTV 596 Query: 594 VRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGTPL 647 + V VEPG TV+AG L+V+EAMKMEH+I AP GVV L G+ V PL Sbjct: 597 LVVKVEPGDTVKAGTPLLVVEAMKMEHTITAPVDGVVSQLDVRAGQQVALDEPL 650 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: 1112 Number of extensions: 51 Number of successful extensions: 5 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: 660 Length adjustment: 38 Effective length of query: 617 Effective length of database: 622 Effective search space: 383774 Effective search space used: 383774 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 Apr 09 2024. 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