GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tynA in Burkholderia phytofirmans PsJN

Align primary-amine oxidase (EC 1.4.3.21) (characterized)
to candidate BPHYT_RS09910 BPHYT_RS09910 tyramine oxidase

Query= BRENDA::A1R2C3
         (656 letters)



>FitnessBrowser__BFirm:BPHYT_RS09910
          Length = 661

 Score =  564 bits (1454), Expect = e-165
 Identities = 292/658 (44%), Positives = 405/658 (61%), Gaps = 12/658 (1%)

Query: 10  ATTQAPLGQHPLEQLSAHEIHQARRILADAGLVAETTRFAYLGLIEPPKAVFQADAADA- 68
           ATT A    HPL+ LS  E+  A  ++  A  +    RF  + L EPPKA   A      
Sbjct: 5   ATTAAHAPFHPLDPLSGAEMQLACDLVKAAEKLDSHARFPMVELREPPKAEVVAFKTGEY 64

Query: 69  -PRLVRAMLWDAAQSRSLDVRLSLATGLVLDQREL--NPEIDGQLPVLLEEFGIIEDILA 125
             R    +  D     +++  + L    +  +R +       GQ P+++++F   E I+ 
Sbjct: 65  FSRTAFVLAIDRTNGATIEFEVDLREKKIAARRVMPFGEAPYGQPPIMIDDFMNAEQIVK 124

Query: 126 VDPQWNAALASRGLTPA---QVRVAPLSAGVFEYGNEEGKRLLRGLGFRQDHPADHPWAH 182
            D  W  A+  RGL+     +V+V P SAG F+  NE G+RL+R + + ++   D+ +AH
Sbjct: 125 SDEAWRVAVMKRGLSEKDLERVQVDPFSAGCFDRENENGRRLVRCVSYYRETLTDNGYAH 184

Query: 183 PIDGLVAFVDIENRRVNHLIDDGPV-PVPEVNGNYTDPTIHGELRTDLKPIEITQPEGPS 241
           PI+G++A VD+  ++V  L+DDG + P+P    NY  P++ GE R+ LKP+ I QP+GPS
Sbjct: 185 PIEGVMAVVDLLEKKVIELVDDGRIIPIPRAKHNYDTPSL-GEPRSTLKPLSIDQPDGPS 243

Query: 242 FTLEGNHLSWAGWDLRVGFDAREGLVLHQLHHSHQGRRRPVVHRASISEMVVPYGDPSPY 301
           FT++G H++W  W+ RVGF  REGLVLHQL        RP+++RAS++EM VPY DP+  
Sbjct: 244 FTIDGWHVNWQNWNFRVGFTPREGLVLHQLSWDDGKSTRPIIYRASVTEMCVPYSDPTTN 303

Query: 302 RSWQNYFDSGEYLVGRDANSLKLGCDCLGDITYMSPVVADDFGNPRVIENGICIHEEDAG 361
             W++ FD+GEY +G+ AN L+LGCDCLG I Y     ADDFGNP V++N +C+HEED G
Sbjct: 304 HYWKSAFDAGEYGLGKLANQLELGCDCLGTIRYFDIPSADDFGNPFVMKNAVCMHEEDYG 363

Query: 362 ILWKHTDEWAGSNEVRRNRRLVVSFFTTVGNYDYGFYWYLYLDGTIEFEAKATGIVFTAA 421
            LWKH +   G  E+RR+RRLV+SFF TVGNYDYGFYWYLY DGTI+ E K TGIV T+A
Sbjct: 364 TLWKHYEFRTGVFEMRRSRRLVISFFATVGNYDYGFYWYLYQDGTIQLECKLTGIVQTSA 423

Query: 422 LPDKD-YAYASEIAPGLGAPYHQHLFSARLDMMVDGGTNRVEELDLVRLPKGPGNPHGNA 480
           + D D Y +   I   LG P HQH F+AR+ MMVDG  N V E + V  P G  NP+GN 
Sbjct: 424 VADGDTYPWGGMITENLGGPTHQHFFNARMHMMVDGERNTVTEHEFVPRPMGENNPYGNV 483

Query: 481 FTQKRTVLTRESEAVRDADGTKGRVWHISNPDSLNHLGHPVGYTLYPEGNPTLAMADDSS 540
           F   + VL  ESEA R+A+G+ GR W +SNP+  N +G   GY L    +P +   + S 
Sbjct: 484 FDTTKRVLKTESEAARNANGSTGRYWKVSNPNVKNAVGANPGYKLVVNDSPLMLADERSK 543

Query: 541 IASRAAFAKHHLWVTQHAEDELYAAGDFVNQHPGGAGLPSYVAQDRDIDGQDLVVWHSFG 600
           +  R  FA  H+WVT     E YA+GD+ NQH GG GLP Y+  +R+I+ +D+V+WHSFG
Sbjct: 544 VRQRGGFATRHVWVTPFDPAERYASGDYPNQHSGGDGLPRYIEANRNIENEDVVLWHSFG 603

Query: 601 LTHFPRPEDWPIMPVDTTGFTLKPHGFFDQNPTLNVPSSSTGHCAPAEQNT--GTCGH 656
            TH  +PED+P+MPV+  GF LKP+ FF  NPT+++P+    +     ++T  G C H
Sbjct: 604 HTHVCKPEDFPVMPVEYAGFMLKPNNFFSANPTMDLPAERDLNSVEDGKSTDHGCCKH 661


Lambda     K      H
   0.319    0.137    0.432 

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: 1403
Number of extensions: 77
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: 656
Length of database: 661
Length adjustment: 38
Effective length of query: 618
Effective length of database: 623
Effective search space:   385014
Effective search space used:   385014
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