Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF2594 HP15_2538 acetyl/propionyl-CoA carboxylase beta subunit
Query= BRENDA::Q9I297 (535 letters) >FitnessBrowser__Marino:GFF2594 Length = 538 Score = 473 bits (1218), Expect = e-138 Identities = 253/542 (46%), Positives = 344/542 (63%), Gaps = 11/542 (2%) Query: 1 MAILHTQINPRSAEFAANAATMLEQVNALRTLLGRIHEGGGSAAQARHSARGKLLVRERI 60 M +L + ++ S +F NA M + R + ++ + AA+ + + RGKLL R+RI Sbjct: 1 MQVLESTVSSTSEDFRTNAEAMDAHITTFRDVEQKVLDLA-EAAREKFTKRGKLLPRDRI 59 Query: 61 NRLLDPGSPFLELSALAAHEVYGEE---VAAAGIVAGIGRVEGVECMIVGNDATVKGGTY 117 NRLLD G+PFLEL +LA ++++ ++ +A GI+AGIG V G+ C++V +++ +KGGT Sbjct: 60 NRLLDRGTPFLELCSLAGYKMHDDKDGSLAGGGIIAGIGYVSGIRCLVVASNSAIKGGTI 119 Query: 118 YPLTVKKHLRAQAIALENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSARG 177 P + K LR Q IA+EN+LP + L +SGGANL ++F R F NQA MSA G Sbjct: 120 TPAGLDKTLRLQQIAMENKLPVVSLSESGGANLNYATDIFVLG---ARGFANQARMSAAG 176 Query: 178 IPQIAVVMGSCTAGGAYVPAMSDETVMVREQATIFLAGPPLVKAATGEVVSAEELGGADV 237 IPQ+ VV G+ TAGGAY P +SD ++VREQA +FLAGPPL+KAATGEV + EELGGA++ Sbjct: 177 IPQVTVVHGNATAGGAYQPGLSDYVIVVREQAKMFLAGPPLLKAATGEVATDEELGGAEM 236 Query: 238 HCKVSGVADHYAEDDDHALAIARRCVANLNWRKQGQLQCRAP-RAPLYPAEELYGVIPAD 296 H V+G A++ AEDD + AR + L W +Q Q PLYPA+EL GVIPAD Sbjct: 237 HATVAGTAEYLAEDDADGIRQARNILEALPWNEQLQPWRELQWEEPLYPADELLGVIPAD 296 Query: 297 SKQPYDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKG 356 SK+PYDVRE++AR+ DGS+F +FK F VCG + G+ + I+ NNG + + K Sbjct: 297 SKKPYDVREILARIADGSKFMDFKNEFDDQTVCGTIRIEGHSVGIIGNNGPITPAGSAKA 356 Query: 357 AHFIELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACARVPKFTVLIGGS 416 A FI+L Q G PLLFL N TGFMVG E GI KHG+K++ AVA RVPK ++IGGS Sbjct: 357 AQFIQLCDQAGTPLLFLHNTTGFMVGTHSEQNGIIKHGSKMIQAVANCRVPKVAIVIGGS 416 Query: 417 FGAGNYGMCGRAYDPRFLWMWPNARIGVMGGEQAAGVLAQVKREQAERAGQQLGVEEEAK 476 +GAGNY MCGR DPRF++ WPN+R VMG QA V+ V ++ R G + + Sbjct: 417 YGAGNYAMCGRGLDPRFIFAWPNSRTAVMGPAQAGKVMRIVAEDKQRRGGMEPDPKTLDF 476 Query: 477 IKAPILEQYEHQGHPYYSSARLWDDGVIDPAQTREVLALALSAALNA---PIEPTAFGVF 533 ++ ++ E + +ARLWDDG+IDP TR VLAL L A + P FGV Sbjct: 477 LEQATAKKLEEGSTALFGTARLWDDGLIDPRDTRRVLALVLDVCREAEARQLRPNTFGVA 536 Query: 534 RM 535 R+ Sbjct: 537 RL 538 Lambda K H 0.321 0.137 0.409 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: 776 Number of extensions: 38 Number of successful extensions: 6 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: 535 Length of database: 538 Length adjustment: 35 Effective length of query: 500 Effective length of database: 503 Effective search space: 251500 Effective search space used: 251500 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 (21.9 bits) S2: 52 (24.6 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