Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA carboxylase biotin-containing subunit; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate CA265_RS18365 CA265_RS18365 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::Q96RQ3 (725 letters) >FitnessBrowser__Pedo557:CA265_RS18365 Length = 446 Score = 421 bits (1082), Expect = e-122 Identities = 211/439 (48%), Positives = 297/439 (67%), Gaps = 3/439 (0%) Query: 51 KVLIANRGEIACRVMRTAKKLGVQTVAVYSEADRNSMHVDMADEAYSIGPAPSQQSYLSM 110 K+LIANRGEIA R++RT K++G++TVAVYS ADR S+HV ADEA IGP PS+ SYL++ Sbjct: 4 KILIANRGEIALRIIRTCKEMGIKTVAVYSTADRESLHVRFADEAVCIGPPPSKDSYLNI 63 Query: 111 EKIIQVAKTSAAQAIHPGCGFLSENMEFAELCKQEGIIFIGPPPSAIRDMGIKSTSKSIM 170 II A+ + A AIHPG GFLSEN +F+ +C++ I FIG P I MG K+++K M Sbjct: 64 PNIISAAELTNADAIHPGYGFLSENAKFSNICREYNIKFIGATPEQINGMGDKASAKETM 123 Query: 171 AAAGVPVVEGYHGEDQSDQCLKEHARRIGYPVMIKAVRGGGGKGMRIVRSEQEFQEQLES 230 AGVP + G G S + A +GYPV++KA GGGG+GMR+V +++F+ +S Sbjct: 124 KIAGVPTIPGSEGLLTSVKEGIAIANEMGYPVILKATAGGGGRGMRVVWKDEDFENAWDS 183 Query: 231 ARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKIIEEAP 290 AR+E+ +F +D + +EK+++ PRH+E+Q+ GD G A +L ERDCS+QRRHQK++EE+P Sbjct: 184 ARQESGAAFGNDGLYLEKYIEDPRHIEIQIIGDQFGKACHLSERDCSIQRRHQKLVEESP 243 Query: 291 APGIKSEVRKKLGEAAVRAAKAVNYVGAGTVEFIMDSKHNFCFMEMNTRLQVEHPVTEMI 350 +P + E+R ++GEAA++ A AVNY GAGT+EF++D NF FMEMNTR+QVEHPVTE + Sbjct: 244 SPFMTDELRVRMGEAAIKGAMAVNYEGAGTIEFLVDKHRNFYFMEMNTRIQVEHPVTEEV 303 Query: 351 TGTDLVEWQLRIAAGEKIPLSQEEITLQGHAFEARIYAEDPSNNFMPVAGPLVHLSTPRA 410 DL++ Q+++AAG IP+S + HA E RI AEDP+NNF P G + + +P Sbjct: 304 INFDLIKEQIKVAAG--IPISGKNYFPDMHAIECRINAEDPANNFRPSPGKITNFHSP-G 360 Query: 411 DPSTRIETGVRQGDEVSVHYDPMIAKLVVWAADRQAALTKLRYSLRQYNIVGLHTNIDFL 470 R++T V G + +YD MIAKL+ A R+ A+ + +L ++ I G+ T I F Sbjct: 361 GHGVRVDTHVYAGYSIPSNYDSMIAKLICVAQTREEAICTMERALGEFVIEGVKTTIPFH 420 Query: 471 LNLSGHPEFEAGNVHTDFI 489 L L P F AGN T F+ Sbjct: 421 LQLMKDPNFRAGNFTTKFM 439 Lambda K H 0.317 0.131 0.377 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: 742 Number of extensions: 22 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: 725 Length of database: 446 Length adjustment: 36 Effective length of query: 689 Effective length of database: 410 Effective search space: 282490 Effective search space used: 282490 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: 53 (25.0 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