Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate Dsui_0982 Dsui_0982 acetyl/propionyl-CoA carboxylase, alpha subunit
Query= reanno::PS:Dsui_0516 (663 letters) >FitnessBrowser__PS:Dsui_0982 Length = 667 Score = 514 bits (1323), Expect = e-150 Identities = 314/679 (46%), Positives = 411/679 (60%), Gaps = 35/679 (5%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60 MF KILIANRGEIACRVIKTAR++GI+TVAVYSEAD +A V +ADEAV +GPAA++ESY Sbjct: 1 MFSKILIANRGEIACRVIKTARRLGIRTVAVYSEADANARHVRLADEAVLLGPAAARESY 60 Query: 61 LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120 LVA+KI+ A ++TGA+A+HPGYGFLSENA+F+ G+ FIGP +I MG K +K Sbjct: 61 LVAEKILDAARRTGAQAIHPGYGFLSENADFAEACAAAGVVFIGPPASAIRAMGSKSAAK 120 Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180 L +A V PGY+ P+ + A IGYPV+IKA+AGGGGKG+R+ + Sbjct: 121 ALMEKAAVPLTPGYHGDNQEPEFLKQQADAIGYPVLIKAAAGGGGKGMRLVDKGEDFIAA 180 Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240 +SC EAR+SFG+D+V +EKY+ PRHIEIQV GDS GN VYL ERDCS+QRRHQKV+E Sbjct: 181 LASCQREARSSFGNDQVLVEKYITRPRHIEIQVFGDSQGNCVYLFERDCSVQRRHQKVLE 240 Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300 EAP+P + PE R+ MGE AVA A+AV Y AGTVEF ++ FYF+EMNTRLQVEHPV Sbjct: 241 EAPAPGMTPERRRQMGEAAVAAAKAVGYVGAGTVEF-IANQDGSFYFMEMNTRLQVEHPV 299 Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360 TE+ITG DLVE +RVA GE LPL Q +QI G A+E RI AED +GFLPSTGRL+ Sbjct: 300 TEMITGQDLVEWQLRVAAGEALPLRQEQLQIRGHALEARIYAEDAGKGFLPSTGRLLHLV 359 Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420 PPAE VRVDTGV +G EI+ +YD MIAKLIV RE A+ARMR AL + + G+++ Sbjct: 360 PPAE-GLNVRVDTGVEEGDEITPHYDPMIAKLIVWDEDREAALARMRQALADYRVVGVTT 418 Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA 480 NI F + L+ F DTG I ++ F S D L VA + R D A Sbjct: 419 NIDFLSRLVSCPAFAGADLDTGLIERQQDFLFPESPEVPRDVILTATVAELLRER--DLA 476 Query: 481 AQVSGQLPGHERKVGDEWVV--IRNGERHPVVAK----------PIEGGYLVTYNGEKYE 528 AQ R+ GD W R+G R + A+ ++ G V Y GE ++ Sbjct: 477 AQ-------QGRRSGDPWSPWNRRDGWRMNIAARRTVSFRVGETQVDVG--VAYAGEDWQ 527 Query: 529 LLSDWRQGQSLFNGTCNG-EEFTLQVERHRMTYQLFHWGTRADMMVMSA----RAAELLA 583 L R L G + +++E R+ + + + + S + L Sbjct: 528 L--TLRNDTLLVRGRLLAHDRLAVELEDRRLMASVVAVAEKRHVFLNSGTYVIERHDPLH 585 Query: 584 LMPEKAAPDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVK 643 L+ +A L +PMPG + + G K G L ++EAMKME+ + A + +K Sbjct: 586 LV--EAGGAQGGGLTAPMPGKVVALLAQPGPVAK-GTPLLILEAMKMEHTITAPKQGNLK 642 Query: 644 KISVTAGSSLSVDEIIIEF 662 G ++ +++F Sbjct: 643 GFRYAVGEQVADGAELVDF 661 Lambda K H 0.319 0.135 0.391 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: 1053 Number of extensions: 44 Number of successful extensions: 5 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: 663 Length of database: 667 Length adjustment: 38 Effective length of query: 625 Effective length of database: 629 Effective search space: 393125 Effective search space used: 393125 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 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