Align Propionyl-CoA carboxylase alpha chain, mitochondrial; PCCase subunit alpha; Propanoyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.3 (characterized)
to candidate GFF2598 HP15_2542 methylcrotonoyl-coenzyme A carboxylase 1 (alpha)
Query= SwissProt::P0DTA4 (730 letters) >FitnessBrowser__Marino:GFF2598 Length = 656 Score = 493 bits (1270), Expect = e-144 Identities = 280/667 (41%), Positives = 393/667 (58%), Gaps = 28/667 (4%) Query: 65 KILIANRGEIACRVIKTCKKMGIKTVAVHSDVDASSVHVTMADEAVCVGPAPTSKSYLNM 124 K+LIANRGEIA RVI+T K +G +TVAV+S+ DA ++HV +ADEAVC+GPA S SYLN Sbjct: 4 KLLIANRGEIAVRVIRTAKALGYRTVAVYSEADAKAMHVELADEAVCIGPAQVSASYLNS 63 Query: 125 DAIMEAVRTTRAQAVHPGYGFLSENKEFAKCLAAEGVIFIGPDTHAIQAMGDKIESKLLA 184 DAI+EA R T A +HPGYGFLSEN FA G++F+GP AI+ MG K SK+ Sbjct: 64 DAILEAARKTGADCIHPGYGFLSENAAFANACKDAGLVFVGPPASAIELMGSKRRSKIAM 123 Query: 185 KKAKVNTIPGFDGVVKDADEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGFRF 244 ++A V +PG++G + DE + A++IGYP+MIKASAGGGG+GMR+ + E D + Sbjct: 124 QEAGVPVVPGYEGNNANDDELIAAAKDIGYPLMIKASAGGGGRGMRLVESESELADNIKR 183 Query: 245 SSQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQKVVEEAP 304 + E+ +FGDD L++EK + PRH+EIQV D+HGNA++L ER+CS+QRR+QKVVEEAP Sbjct: 184 ARSESKQAFGDDELILEKAVIEPRHVEIQVFADRHGNAVYLGERDCSVQRRHQKVVEEAP 243 Query: 305 SIFLDSETRRAMGEQAVALAKAVNYSSAGTVEFLVDSKKNFYFLEMNTRLQVEHPVTECI 364 S F+ E R+AMGE AV A A NY AGTVEFLVD +NFYFLEMNTRLQVEHPVTE I Sbjct: 244 SPFVTPELRQAMGEAAVKAALACNYEGAGTVEFLVDKHRNFYFLEMNTRLQVEHPVTELI 303 Query: 365 TGLDLVQEMIRVAKGYPLRHRQADIPINGWAVECRVYAEDPYKSFGLPSIGRLSQYQEPI 424 TG DLV + VA+G PL Q DI +NG A+E R+YAEDP F P G L + EP Sbjct: 304 TGQDLVAWQLNVAEGRPLPLSQDDIHLNGHAIEVRLYAEDPAHGF-TPQTGSLYAF-EPA 361 Query: 425 HLPGVRVDSGIQPGSDISIYYDPMISKLITYGSNRMEALKRMENALDNYVIRGVTHNIAL 484 G+R D+G++ G I+ +YDPM++K+I +G NR EA +R+ +L++ + GVT N Sbjct: 362 EGEGLRFDTGVRSGDAITPHYDPMLAKVIAWGQNRDEARRRLIRSLEDTTVFGVTTNRHF 421 Query: 485 LREVIINSRFVEGDINTKFLSDVYPD--GFKGHKLTEDERNQLLAIASSLFVASQLRAQR 542 L +I + F G T FL + D + LT + LA+A+ + Sbjct: 422 LSRIIADETFGAGGATTAFLQQAFKDDPSLQPQNLTIRQ----LALAACVLDHGISGQSA 477 Query: 543 FQEPENSRVPIIKPQVANWELSIRLHDEVHTVTASNSGPTFSVEVDGSKLNVTSTWNLAS 602 + + PI + D + + SG SV + ++ ++ Sbjct: 478 WSNAPATMTPI----------KLETGDTTVELLVTRSGSRLSVSMGETRHSLVLESQRDG 527 Query: 603 PLLSVSIDGTQRTIQCLSRDAGGNMSIQFLGTVYKVHILTKLAAELNKFMLEKAAEDTSS 662 L + +G ++ C G ++ +Q G + V +T A A S Sbjct: 528 HLCIID-NGVRQA--CQYHRQGDSLYLQAFGQSWSVRDVTHQPA-------RTAGGAGSG 577 Query: 663 ILHSPMPGVVVAVSVKPGDLVAEGQEICVIEAMKMQNSMTAGKTGKVKSVHCKAGDTVGE 722 + + M G ++ V V+ G V +G + ++EAMKM++ + A + G+V + GD V Sbjct: 578 RIQATMDGAIIDVLVEAGQSVHQGDTLVILEAMKMEHPVKADRDGRVAEILASKGDQVKR 637 Query: 723 GDLLVEL 729 LLV++ Sbjct: 638 SQLLVQI 644 Lambda K H 0.318 0.134 0.385 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: 1103 Number of extensions: 45 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 730 Length of database: 656 Length adjustment: 39 Effective length of query: 691 Effective length of database: 617 Effective search space: 426347 Effective search space used: 426347 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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