GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Burkholderia phytofirmans PsJN

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate BPHYT_RS25975 BPHYT_RS25975 urea carboxylase

Query= reanno::PS:Dsui_0516
         (663 letters)



>FitnessBrowser__BFirm:BPHYT_RS25975
          Length = 1203

 Score =  390 bits (1001), Expect = e-112
 Identities = 214/445 (48%), Positives = 289/445 (64%), Gaps = 5/445 (1%)

Query: 2   FKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYL 61
           F+K+LIANRGEIACRVI+T +++GI +VAVYSEAD+ A+ V +ADEAVCIGPA + +SYL
Sbjct: 3   FRKVLIANRGEIACRVIRTLKRLGIASVAVYSEADRHAMHVMLADEAVCIGPALAAQSYL 62

Query: 62  VADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKK 121
            +  I+ A +  GA+AVHPGYGFLSENA F++  ++ GI+FIGP    + + G K  +++
Sbjct: 63  NSAAILDAARACGADAVHPGYGFLSENAAFAQACDDAGIRFIGPTPQHMREFGLKHTARE 122

Query: 122 LAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGF 181
           LA    V  +PG    +    AA+  A+ IGYPVM+K++AGGGG G+ +  + A+    F
Sbjct: 123 LAQANDVALLPG-TGLLPDVSAALREAESIGYPVMLKSTAGGGGIGMSLCRDAAQLEGVF 181

Query: 182 SSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEE 241
           +S       +F +  V++EK+V   RHIE+QV GD  G  + L ERDCS+QRR+QKVIEE
Sbjct: 182 ASVARLGEANFANAGVYVEKFVENARHIEVQVFGDGKGGVISLGERDCSVQRRNQKVIEE 241

Query: 242 APSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVT 301
            P+P +    R A+   AV LA+AV Y+SAGTVEFV    T+ FYFLE+NTRLQVEH VT
Sbjct: 242 TPAPGLTHAERSALHASAVRLAQAVKYKSAGTVEFVFDADTRRFYFLEVNTRLQVEHCVT 301

Query: 302 ELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQP 361
           E ITG+DLVE MIR A GE  PL        G +++ R+ AEDP + F PS G L     
Sbjct: 302 EEITGIDLVEWMIREAEGELAPLDTLATVPQGASIQVRLYAEDPHKQFQPSAGVLTHVAF 361

Query: 362 PAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISSN 421
            A+     RVDT V  G E+S +YD ++AKLIV G +RE  +A +R AL    + GI +N
Sbjct: 362 AAD----ARVDTWVDSGTEVSAFYDPLLAKLIVKGETREAGLAALRAALEQTQLYGIETN 417

Query: 422 IPFQAALMQHARFQSGIFDTGFIAK 446
           + +  A+   A F  G   T F+ +
Sbjct: 418 LDYLRAIAGSATFARGEQTTAFLGR 442



 Score = 31.2 bits (69), Expect = 3e-04
 Identities = 15/57 (26%), Positives = 34/57 (59%)

Query: 597  LLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSL 653
            +++ + G + ++ V  G+ V  G+ +A++E+MKME  + A  D  ++ I    G+++
Sbjct: 1123 IVADVSGSVWKLLVKEGERVGDGQVVAIVESMKMEISVTASGDGVIETIDCAEGAAV 1179


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: 1746
Number of extensions: 82
Number of successful extensions: 4
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: 1203
Length adjustment: 43
Effective length of query: 620
Effective length of database: 1160
Effective search space:   719200
Effective search space used:   719200
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: 56 (26.2 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