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

GapMind for catabolism of small carbon sources

Aligments 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources