Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate Ac3H11_2275 Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3)
Query= reanno::PS:Dsui_0516 (663 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2275 Length = 682 Score = 901 bits (2328), Expect = 0.0 Identities = 477/683 (69%), Positives = 542/683 (79%), Gaps = 21/683 (3%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60 MF KILIANRGEIACRVI TARKMGI TVAVYS+ADK+A V++ADEAV IG A S+ESY Sbjct: 1 MFTKILIANRGEIACRVIATARKMGIATVAVYSDADKEARHVKLADEAVHIGAAPSRESY 60 Query: 61 LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120 L+ADKIIAACKQTGA+AVHPGYGFLSEN F++R E+EGI FIGPK +SIA MGDKI SK Sbjct: 61 LLADKIIAACKQTGAQAVHPGYGFLSENEAFAKRCEDEGIAFIGPKAHSIAAMGDKIASK 120 Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180 KLA EAKVNTIPGYNDAI GP+ AVEIAK IGYPVMIKASAGGGGKGLRVA+ND EA EG Sbjct: 121 KLANEAKVNTIPGYNDAIAGPEQAVEIAKGIGYPVMIKASAGGGGKGLRVAFNDKEAFEG 180 Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240 F+SC NEARNSFGDDR+FIEK+V EPRHIEIQVLGDSHGN +YLNER+CSIQRRHQKVIE Sbjct: 181 FASCQNEARNSFGDDRIFIEKFVQEPRHIEIQVLGDSHGNVIYLNERECSIQRRHQKVIE 240 Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300 EAPSPF+ RKAMGEQAV LA+AV Y+SAGTVEFVV G ++FYFLEMNTRLQVEHPV Sbjct: 241 EAPSPFISDATRKAMGEQAVQLAKAVKYQSAGTVEFVV-GKDQDFYFLEMNTRLQVEHPV 299 Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360 TE ITGLDLVE MIRVA GEKLPLTQADV+ +GWA+ECRINAEDPFR FLPSTGRLV+FQ Sbjct: 300 TECITGLDLVELMIRVAAGEKLPLTQADVKRDGWAIECRINAEDPFRNFLPSTGRLVRFQ 359 Query: 361 PPAEVDGQ--------VRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNG 412 PP E Q VRVDTGVY+GGEI MYYDSMIAKLIVHG R AIA+MR ALNG Sbjct: 360 PPEETMFQSDTTKKLGVRVDTGVYEGGEIPMYYDSMIAKLIVHGTDRNDAIAKMRAALNG 419 Query: 413 FVIRGISSNIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFV 472 FVIRGISSNIPFQAAL+ H +F +G F+TGFIA+ Y KGF A VPH DP L+ +AAF+ Sbjct: 420 FVIRGISSNIPFQAALLAHPKFVTGDFNTGFIAENYGKGFHAEDVPHSDPMFLVALAAFM 479 Query: 473 HRRYIDRAAQVSGQLPGHERKVGDEWVVIRNG-----ERHPVVAKPIE---GGYLVTYNG 524 HRRY RA+ +SGQL GHE KVG+E+VV+ G + H V E G + Sbjct: 480 HRRYRARASGISGQLAGHEVKVGEEFVVVTLGAEGQNQHHAVTVSDFEDKSGSSAIQVGD 539 Query: 525 EKYELLSDWRQGQSLFNGTCNGEEFTLQVER----HRMTYQLFHWGTRADMMVMSARAAE 580 Y++ S+ GQ G CNG+ FT QVER + + ++ H GT+ D +V+S A+ Sbjct: 540 SSYQISSNATLGQIRVQGACNGQGFTAQVERGVGKNPLALRIAHNGTQIDTLVLSPLGAK 599 Query: 581 LLALMPEKAAPDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDC 640 L LMP KA PDLSKFLLSPMPGLL +V+V GQ+V+AGEKLAVIEAMKMENIL A QD Sbjct: 600 LHKLMPFKAPPDLSKFLLSPMPGLLVDVAVQPGQKVQAGEKLAVIEAMKMENILFAAQDG 659 Query: 641 KVKKISVTAGSSLSVDEIIIEFE 663 V KI+ G SL+VD+II+EF+ Sbjct: 660 VVGKITAGKGESLAVDQIILEFQ 682 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: 1326 Number of extensions: 51 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: 663 Length of database: 682 Length adjustment: 39 Effective length of query: 624 Effective length of database: 643 Effective search space: 401232 Effective search space used: 401232 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