GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Acidovorax sp. GW101-3H11

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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