Alignments for a candidate for puo in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for puo in Burkholderia phytofirmans PsJN

Align Primary amine oxidase 1; AtAO1; EC 1.4.3.21 (characterized)
to candidate BPHYT_RS09910 BPHYT_RS09910 tyramine oxidase

Query= SwissProt::O23349
         (650 letters)



>FitnessBrowser__BFirm:BPHYT_RS09910
          Length = 661

 Score =  261 bits (668), Expect = 5e-74
 Identities = 195/653 (29%), Positives = 309/653 (47%), Gaps = 57/653 (8%)

Query: 22  FHPLDPLTPQEINKTSFIVKKSHLGNLKDLTFHYLDLEEPNKSHVLQWLSPNPSKKPPPP 81
           FHPLDPL+  E+     +VK +   +     F  ++L EP K+ V+ +      K     
Sbjct: 13  FHPLDPLSGAEMQLACDLVKAAEKLD-SHARFPMVELREPPKAEVVAF------KTGEYF 65

Query: 82  RRRSFVVV--RAGGQTYELIIDLTTSKIASSRIY----TGHGFPSFTFIELFKASKLPLT 135
            R +FV+   R  G T E  +DL   KIA+ R+       +G P     +   A ++  +
Sbjct: 66  SRTAFVLAIDRTNGATIEFEVDLREKKIAARRVMPFGEAPYGQPPIMIDDFMNAEQIVKS 125

Query: 136 YPPFKKSILDRSLN---ISEVSCIPFTVGWYGETTT--RRELKASCFYRDGSV-NVFTRP 189
              ++ +++ R L+   +  V   PF+ G +       RR ++   +YR+    N +  P
Sbjct: 126 DEAWRVAVMKRGLSEKDLERVQVDPFSAGCFDRENENGRRLVRCVSYYRETLTDNGYAHP 185

Query: 190 IEGITVTIDVDSMQVIKYSDRFRK-PIPDKEGN-------DFRTKHRPFPFFCNVSDTGF 241
           IEG+   +D+   +VI+  D  R  PIP  + N       + R+  +P           F
Sbjct: 186 IEGVMAVVDLLEKKVIELVDDGRIIPIPRAKHNYDTPSLGEPRSTLKPLSID-QPDGPSF 244

Query: 242 KILGNRVKWANWKFHVGFTARAGVTISTASVLDPRTKRFRRVMYRGHVSETFVPYMDPTY 301
            I G  V W NW F VGFT R G+ +   S  D ++ R   ++YR  V+E  VPY DPT 
Sbjct: 245 TIDGWHVNWQNWNFRVGFTPREGLVLHQLSWDDGKSTR--PIIYRASVTEMCVPYSDPTT 302

Query: 302 EWYYRTFMDIGEFGFGRSAVNLQPLIDCPQNAAFLDGHVAGPDGTAQKMTNVMCVFEKNG 361
             Y+++  D GE+G G+ A  L+   DC     + D   A   G    M N +C+ E++ 
Sbjct: 303 NHYWKSAFDAGEYGLGKLANQLELGCDCLGTIRYFDIPSADDFGNPFVMKNAVCMHEED- 361

Query: 362 YGASFRHTEINVPGQVITSGEAEISLVVRMVATLGNYDYIVDWEFKKNGAIRVGVDLTGV 421
           YG  ++H E       +        LV+   AT+GNYDY   W   ++G I++   LTG+
Sbjct: 362 YGTLWKHYEFRTG---VFEMRRSRRLVISFFATVGNYDYGFYWYLYQDGTIQLECKLTGI 418

Query: 422 LEVKATS----YTSNDQITENVYGTLVAKNTIAVNHDHYLTYYLDLDVDGNGNSLVKAKL 477
           ++  A +    Y     ITEN+ G           H H+    + + VDG  N++ + + 
Sbjct: 419 VQTSAVADGDTYPWGGMITENLGGP---------THQHFFNARMHMMVDGERNTVTEHEF 469

Query: 478 KTVRVTEVNKTSSRRKSYWTVVKETAKTEADG-RVRLGSDPVELLIVNPNKKTKIGNTVG 536
               + E N   +     +   K   KTE++  R   GS      + NPN K  +G   G
Sbjct: 470 VPRPMGENNPYGN----VFDTTKRVLKTESEAARNANGSTGRYWKVSNPNVKNAVGANPG 525

Query: 537 YRLIPEHLQATSLLTDDDYPELR--AGYTKYPVWVTAYDRSERWAGGFYSDRSRGDDGLA 594
           Y+L+   +  + L+  D+  ++R   G+    VWVT +D +ER+A G Y ++  G DGL 
Sbjct: 526 YKLV---VNDSPLMLADERSKVRQRGGFATRHVWVTPFDPAERYASGDYPNQHSGGDGLP 582

Query: 595 VWSSRNREIENKDIVMWYNVGFHHIPYQEDFPVMPTLHGGFTLRPSNFFDNDP 647
            +   NR IEN+D+V+W++ G  H+   EDFPVMP  + GF L+P+NFF  +P
Sbjct: 583 RYIEANRNIENEDVVLWHSFGHTHVCKPEDFPVMPVEYAGFMLKPNNFFSANP 635


Lambda     K      H
   0.320    0.138    0.424 

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: 1204
Number of extensions: 60
Number of successful extensions: 9
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: 650
Length of database: 661
Length adjustment: 38
Effective length of query: 612
Effective length of database: 623
Effective search space:   381276
Effective search space used:   381276
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: 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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Protein sequences (fasta format)
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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
the source code
instructions for running GapMind on your computer

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