Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate GFF2594 HP15_2538 acetyl/propionyl-CoA carboxylase beta subunit
Query= metacyc::MONOMER-17283 (535 letters) >FitnessBrowser__Marino:GFF2594 Length = 538 Score = 424 bits (1091), Expect = e-123 Identities = 227/545 (41%), Positives = 326/545 (59%), Gaps = 17/545 (3%) Query: 1 MSIIHSHIQPNSPDFQAN---FAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVR 57 M ++ S + S DF+ N H + D+ +++ + + R + +RGKL R Sbjct: 1 MQVLESTVSSTSEDFRTNAEAMDAHITTFRDVEQKVLDLAEAA----REKFTKRGKLLPR 56 Query: 58 DRIDTLIDPDSSFLEIGALAAYNVYDEE---VPAAGIVCGIGRVAGRPVMIIANDATVKG 114 DRI+ L+D + FLE+ +LA Y ++D++ + GI+ GIG V+G +++A+++ +KG Sbjct: 57 DRINRLLDRGTPFLELCSLAGYKMHDDKDGSLAGGGIIAGIGYVSGIRCLVVASNSAIKG 116 Query: 115 GTYFPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMS 174 GT P + K LR Q+IA EN+LP + L +SGGA L +++F R F NQA+MS Sbjct: 117 GTITPAGLDKTLRLQQIAMENKLPVVSLSESGGANLNYATDIFVLG---ARGFANQARMS 173 Query: 175 AEGIPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGG 234 A GIPQ+ V G+ TAGGAY P +SD V++V+ +FL GPPL+KAATGE T EELGG Sbjct: 174 AAGIPQVTVVHGNATAGGAYQPGLSDYVIVVREQAKMFLAGPPLLKAATGEVATDEELGG 233 Query: 235 ADVHTRISGVADYFANDDREALAIVRDIVAHLGPRQRAN-WELRDPEPPRYDPREIYGIL 293 A++H ++G A+Y A DD + + R+I+ L ++ W E P Y E+ G++ Sbjct: 234 AEMHATVAGTAEYLAEDDADGIRQARNILEALPWNEQLQPWRELQWEEPLYPADELLGVI 293 Query: 294 PRDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESA 353 P D ++ YDVRE++ARI DGS+ +FK + VCG IEG VGI+ NNG + + Sbjct: 294 PADSKKPYDVREILARIADGSKFMDFKNEFDDQTVCGTIRIEGHSVGIIGNNGPITPAGS 353 Query: 354 LKGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVII 413 K A FI+LC PL+FL N TGFMVG E GI K G+K++ AV+ VPK ++I Sbjct: 354 AKAAQFIQLCDQAGTPLLFLHNTTGFMVGTHSEQNGIIKHGSKMIQAVANCRVPKVAIVI 413 Query: 414 GGSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEE 473 GGS+GAGNY MCGR PR ++ WPN+R +VMG QA V+ + D R G + P+ Sbjct: 414 GGSYGAGNYAMCGRGLDPRFIFAWPNSRTAVMGPAQAGKVMRIVAEDKQRRGGMEPDPKT 473 Query: 474 QERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEA---PVQPTRF 530 + K E+ + +ARLWDDG+IDP +TRRVLAL L EA ++P F Sbjct: 474 LDFLEQATAKKLEEGSTALFGTARLWDDGLIDPRDTRRVLALVLDVCREAEARQLRPNTF 533 Query: 531 GVFRM 535 GV R+ Sbjct: 534 GVARL 538 Lambda K H 0.322 0.139 0.423 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: 768 Number of extensions: 43 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: 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