Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_012469656.1 GLOV_RS07900 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::pseudo5_N2C3_1:AO356_01595 (649 letters) >NCBI__GCF_000020385.1:WP_012469656.1 Length = 446 Score = 447 bits (1150), Expect = e-130 Identities = 226/440 (51%), Positives = 307/440 (69%), Gaps = 2/440 (0%) Query: 9 LLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68 +L+ANRGEIA RV+R + +G+ TVAV+S D D+ H + AD V +G + ++ SYL I+ Sbjct: 5 ILIANRGEIAIRVIRACKELGIKTVAVYSTADADSLHVKLADESVCIGPAPSSQSYLNIN 64 Query: 69 KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKTLME 128 +I+AA+ + A+AIHPGYGFLSENA FA E G+ F+GP A ++ MG K +A+ + Sbjct: 65 AIISAAELTDAEAIHPGYGFLSENAKFAEICEQCGITFIGPSAESMRVMGDKISARQAVI 124 Query: 129 TAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188 GVP++PG + ++ A++IG+PV++KATAGGGG+GMK+V + LA A A+A Sbjct: 125 EHGVPILPGTKENVKTVDEAVKIAKQIGFPVIIKATAGGGGRGMKIVHSQATLANAYATA 184 Query: 189 QREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248 + EAQ+ FG+ + +EKY ++PRHVEIQV AD+HGNC++L ERDCSIQRRHQK++EEAP Sbjct: 185 KAEAQAGFGNPDVYIEKYCVEPRHVEIQVLADKHGNCIHLGERDCSIQRRHQKIIEEAPC 244 Query: 249 PGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 308 P LTP+ R+AMG+AA++AA+A+ Y GTVEFLLD GEF+FMEMNTR+QVEHPVTE IT Sbjct: 245 PVLTPETRKAMGDAAIKAAKAVNYSSVGTVEFLLDKSGEFYFMEMNTRIQVEHPVTEMIT 304 Query: 309 GLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLALYRESAEG 368 G+DL+ QIR A G PL Q + + GHAIE R+ AEDP F P G++ Y + G Sbjct: 305 GVDLIREQIRSAAGLPLRYKQEDIKITGHAIECRINAEDPFK-FTPCPGKITAYHQPG-G 362 Query: 369 PGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGLKTNIGFLR 428 G RVDS V + + P YD M+GKLI E RE A R+ LDE++I G+KT I F + Sbjct: 363 LGVRVDSFVYDQYTVVPHYDSMIGKLIVHAETREDAIRRMARALDEYIIEGIKTTIFFHK 422 Query: 429 RIVAHPAFAAAELDTGFIPR 448 RI+ + F +DT F+ R Sbjct: 423 RIMTNKDFIEGNVDTSFLDR 442 Lambda K H 0.319 0.134 0.390 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: 716 Number of extensions: 28 Number of successful extensions: 2 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: 649 Length of database: 446 Length adjustment: 35 Effective length of query: 614 Effective length of database: 411 Effective search space: 252354 Effective search space used: 252354 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 (21.7 bits) S2: 52 (24.6 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