Alignments for a candidate for puo in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for puo in Herbaspirillum seropedicae SmR1

Align Primary amine oxidase 1; AtAO1; EC 1.4.3.21 (characterized)
to candidate HSERO_RS17625 HSERO_RS17625 tyramine oxidase

Query= SwissProt::O23349
         (650 letters)



>FitnessBrowser__HerbieS:HSERO_RS17625
          Length = 748

 Score =  291 bits (745), Expect = 7e-83
 Identities = 199/647 (30%), Positives = 301/647 (46%), Gaps = 37/647 (5%)

Query: 23  HPLDPLTPQEINKTSFIVKKSHLGNLKDLTFHYLDLEEPNKSHVLQWLSPNPSKKPPPPR 82
           HPL+PL+  EIN    ++K S      +  F  + L EP K  V  W      +     R
Sbjct: 115 HPLNPLSADEINAALEVLKASGRWQ-PNYRFTEITLAEPPKEQV--WKFALGERGQTIAR 171

Query: 83  RRSFVVVRAGGQTYELIIDLTTSKIASSRIYTGHGFPSFTFIELFKASKLPL-TYPPFKK 141
           R  F ++  G +  E  +DL    +  +R     G      ++ F   +  + + P + +
Sbjct: 172 RADFTLLD-GSKVIEGTVDLGQRNV--TRWEPKEGVHGMVLVDDFATVQNAMESSPEYAQ 228

Query: 142 SILDRSL-NISEVSCIPFTVGWYGETTTRRE----LKASCFYRDGSVNVFTRPIEGITVT 196
           ++  R + +I +V   P TVG++G     +E    LK   +   G  N +  PIE +   
Sbjct: 229 ALAKRGITDIKKVVATPLTVGYFGGKDALQEDARLLKVVSYLDVGDGNYWAHPIENLVAV 288

Query: 197 IDVDSMQVIKYSDRFRKPIPDK----EGNDFRTKHRPFPFFCNVSD-TGFKILGNRVKWA 251
           +D+   +VIK  D    P+P K    +G+       P P   +  +   + I GN ++W 
Sbjct: 289 VDLVQKKVIKIEDNGVIPVPMKPTGYDGSGRALVPPPKPLDISEPEGKNYTITGNTLRWR 348

Query: 252 NWKFHVGFTARAGVTISTASVLDPRTKRFRRVMYRGHVSETFVPYMDPTYEWYYRTFMDI 311
           NW+ H    +R G+  ST +  D   KR  ++MY G +    VPY DP   WY++ ++D 
Sbjct: 349 NWEMHFKLDSRVGLMFSTVTYNDHGKKR--QIMYEGSLGGMIVPYGDPDVGWYFKAYLDS 406

Query: 312 GEFGFGRSAVNLQPLIDCPQNAAFLDGHVAGPDGTAQKMTNVMCVFEKNGYGASFRHTEI 371
           GE+G G     ++   D P N   LD  +A   G  + +   + VFE+   G  F+H E 
Sbjct: 407 GEYGMGTLTSPIERGKDAPDNVVLLDATLADTSGKPRTIPRAIGVFERYA-GPEFKHQEY 465

Query: 372 NVPGQVITSGEAEISLVVRMVATLGNYDYIVDWEFKKNGAIRVGVDLTGVLEVKAT-SYT 430
             P   +   E    LV+R ++T+GNYDYI DW F +NG I +    TG+  VK   S T
Sbjct: 466 GQPNLSVERRE----LVIRWISTVGNYDYIFDWVFAENGTIGINAGATGIEAVKGVKSST 521

Query: 431 SNDQIT--ENVYGTLVAKNTIAVNHDHYLTYYLDLDVDGNGNSLVKAKLKTVRVTEVNKT 488
             D     +  YGTL+  N +   H H   + LDLDVDG  NSL +       V   N  
Sbjct: 522 MRDASAAEDTRYGTLIDHNIVGTTHQHIYNFRLDLDVDGQNNSLTEVD----PVVLPNTP 577

Query: 489 SSRRKSYWTVVKETAKTEADGRVRLGSDPVELLIVNPNKKTKIGNTVGYRLIP-----EH 543
              R S    V+ TA+TE     +  +  + LL  NPNK  K+GN V Y+LIP       
Sbjct: 578 GGPRSSTMQTVQRTAETEQQAAQKFDASTIRLLS-NPNKFNKVGNPVSYQLIPYAGGTHP 636

Query: 544 LQATSLLTDDDYPELRAGYTKYPVWVTAYDRSERWAGGFYSDRSRGDDGLAVWSSRNREI 603
           +   +  + D++   R  +    +WVT YD  +R+  G Y +RS  D GL  +   N+ I
Sbjct: 637 IAKGANFSPDEWLNKRLSFMDRQLWVTRYDPQQRFPEGKYPNRSHEDTGLGAFVKDNQSI 696

Query: 604 ENKDIVMWYNVGFHHIPYQEDFPVMPTLHGGFTLRPSNFFDNDPLIG 650
            N+D V+W   G  H+   E++P+MPT      L+P NFFD  P +G
Sbjct: 697 VNQDDVVWLTTGTTHVARAEEWPIMPTEWVHVLLKPWNFFDETPTLG 743


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: 1207
Number of extensions: 69
Number of successful extensions: 8
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: 748
Length adjustment: 39
Effective length of query: 611
Effective length of database: 709
Effective search space:   433199
Effective search space used:   433199
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