GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ2 in Burkholderia phytofirmans PsJN

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate BPHYT_RS13360 BPHYT_RS13360 aldehyde dehydrogenase

Query= BRENDA::P77455
         (681 letters)



>FitnessBrowser__BFirm:BPHYT_RS13360
          Length = 531

 Score =  409 bits (1052), Expect = e-118
 Identities = 229/521 (43%), Positives = 317/521 (60%), Gaps = 14/521 (2%)

Query: 4   LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63
           L + ++G W +G G    +   ++G AL  V+SEGLD+A A  FA + G  ALRA+T+ +
Sbjct: 5   LKNHVAGQWIAGSGTGVTLTDPVTGVALVRVSSEGLDLAHAFGFARDTGGAALRALTYAQ 64

Query: 64  RAAMLKAVAKHLLSEKERFYALS-AQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDT 122
           RAA L  + K L ++++ +YA++ A +G TR DS VDI+GGI TL  YA LG+  L D  
Sbjct: 65  RAARLADIVKLLQAKRDDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGA-SLGDVH 123

Query: 123 LWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKP 182
              + E + LSK+  F+ +H+LT   GVA+ INAFNFP WG+ EK AP  L G+P I+KP
Sbjct: 124 ALRDGESVSLSKDQSFSVQHVLTPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVKP 183

Query: 183 ATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRV 242
           ATATA LTQ MV  +VD+G++P GA+S+ICGS+  LLD + S DVV+FTGSA T   LR 
Sbjct: 184 ATATAWLTQRMVADVVDAGILPPGALSVICGSSAGLLDQIQSFDVVSFTGSAQTAATLRA 243

Query: 243 QPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRII 302
            P  V +     +EADSLN  +L  D  P  P F LFI+EVVREMT K+GQKCTAIRR  
Sbjct: 244 HPAFVQRGARLNVEADSLNSAILCADAAPGTPAFDLFIKEVVREMTVKSGQKCTAIRRAF 303

Query: 303 VPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRL 362
           VP+  + AV +AL A+L K+ VGDP  + V+MG+LV+ EQ  +V   +  L         
Sbjct: 304 VPEGALEAVLEALNAKLAKITVGDPRNDTVRMGSLVSREQYENVLAGIAALREEAVLAFD 363

Query: 363 GGQADL----SAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQ--------NQR 410
           G    L    S   A   P L     PD    +H  E FGPVA++ P +         + 
Sbjct: 364 GSAVPLIDADSNIAACIAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVATDAATLPEA 423

Query: 411 HALQLACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQL 470
           HA+ LA  G GSL  ++ + D     +   + A +HGR+  ++    +  TGHG+ +P  
Sbjct: 424 HAVALARRGQGSLVASIYSNDEAHLGRLALELADSHGRVHAISPSVQQSQTGHGNVMPMS 483

Query: 471 VHGGPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISK 511
           +HGGPGRAGGGEELGGLRA+  Y +R+A+Q +   + ++++
Sbjct: 484 LHGGPGRAGGGEELGGLRALGFYHRRSAIQAASAAIGSLTQ 524


Lambda     K      H
   0.319    0.134    0.395 

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: 803
Number of extensions: 36
Number of successful extensions: 5
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: 681
Length of database: 531
Length adjustment: 37
Effective length of query: 644
Effective length of database: 494
Effective search space:   318136
Effective search space used:   318136
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 (21.8 bits)
S2: 53 (25.0 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