Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_027457190.1 K420_RS0105525 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::pseudo6_N2E2:Pf6N2E2_2194 (649 letters) >NCBI__GCF_000519045.1:WP_027457190.1 Length = 667 Score = 491 bits (1265), Expect = e-143 Identities = 290/669 (43%), Positives = 405/669 (60%), Gaps = 35/669 (5%) Query: 9 LLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68 +L+ANRGEIACRV++TA+ MG+ TVAV+S D+DA H AD V +G + + +SYL +D Sbjct: 5 ILIANRGEIACRVIKTARKMGIATVAVYSEADKDALHVDLADEAVCIGPAASKESYLVMD 64 Query: 69 KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKALME 128 K+IAA K +GA+A+HPGYGFLSENA F+R +E G+ F+GP ++ MG K +K L Sbjct: 65 KIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSVAKMGDKIESKKLAI 124 Query: 129 TAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188 A V +PGY+ + A++IGYPV++KA+AGGGGKG++V + ++ E +S Sbjct: 125 EAKVNTIPGYNDAIAGPAEAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAFEGFSSC 184 Query: 189 QREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248 EA++SFGD R+ +EKY+L+PRH+EIQV D HGN +YLNERDCSIQRRHQKV+EEAP+ Sbjct: 185 VNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEEAPS 244 Query: 249 PGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLD-ARGEFFFMEMNTRLQVEHPVTEAI 307 P + ++R+AMGE AV A+A+ Y AGTVEF++ A EF+F+EMNTRLQVEHPVTE I Sbjct: 245 PFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVTELI 304 Query: 308 TGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPVNDFLPATGRLALYRESAK 367 TGLDLV IRVA GE LP+TQA V + G A+E R+ AEDP FLP+TGRL ++ + Sbjct: 305 TGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQPPKE 364 Query: 368 GPGR-RVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGLKTNIGF 426 PG+ RVD+GV +G EIS FYD M+ KLI G REQA R+ L+ F I G+ +NI F Sbjct: 365 IPGQVRVDTGVYDGGEISMFYDSMIAKLIVHGATREQAIARMRDALNGFVIRGISSNIPF 424 Query: 427 LRRIVAHPAFAAAELDTGFIPR-----YQAQLLP--EPGELDD--AFWLAAAQGFALSLA 477 ++ HP F + DTGFIP+ + A ++P +P L A+ A + S++ Sbjct: 425 QAALMQHPVFHSGIFDTGFIPKHYPTGFDASMVPHDDPALLVSVAAYVYRAYTDRSASVS 484 Query: 478 PHIRGDD--AGSPWASTTGMRLGLSRETT--------LHLSCEGQDRALTLD----VTAH 523 ++G + G W + G H+ +G+ + D + Sbjct: 485 GQLQGHERIVGDQWMVVRLNKEGNEHHEVTARPIPGGYHVEYKGEQYEILSDWKLGESLF 544 Query: 524 CAELKGERLT--IEHHGVRRS--HRAIRQGDSLYLHWAGDLHRIDLYDPLAAAEASHSHQ 579 GE T +E H + S H R + A +L + L A + S Sbjct: 545 NGTCNGEEFTLQVERHKTKYSLFHWGTRADFMVMSARAAEL--LALMPEKPAPDLSKF-- 600 Query: 580 GGLAAPMNGSIVRVLVSVGQPVDAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVS 639 L +PM G + + V VGQ V AG +L V+EAMKME+ ++A + +K + GE +S Sbjct: 601 --LLSPMPGLLREIAVQVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISAAVGESLS 658 Query: 640 EGSALVAFE 648 ++ FE Sbjct: 659 VDQIIIEFE 667 Lambda K H 0.319 0.134 0.389 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: 1002 Number of extensions: 44 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 649 Length of database: 667 Length adjustment: 38 Effective length of query: 611 Effective length of database: 629 Effective search space: 384319 Effective search space used: 384319 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: 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