GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aruH in Herbaspirillum seropedicae SmR1

Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate HSERO_RS15115 HSERO_RS15115 aminotransferase

Query= BRENDA::Q9HUI9
         (393 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS15115 HSERO_RS15115
           aminotransferase
          Length = 385

 Score =  157 bits (396), Expect = 6e-43
 Identities = 113/355 (31%), Positives = 176/355 (49%), Gaps = 12/355 (3%)

Query: 37  LSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAVD-AEQV 95
           L  G PDF     +V A   ++  G   Y  + G   LR+ IAE+  +  G   D   ++
Sbjct: 33  LGQGFPDFHCDPALVAAVTQAMQEGLNQYPPMAGVPVLREAIAEKVEKLYGHRYDPVSEI 92

Query: 96  VVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSE---NGFR 152
            V AGA   +   V C ++PGDEVIV EP+Y  Y       G   VPV V+ E    G+ 
Sbjct: 93  TVTAGATQGILTSVLCAVHPGDEVIVIEPVYDCYVPAIELAGG--VPVFVQMEVGAQGYS 150

Query: 153 VQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELLF 212
           +  ++V A +TP+TR + +N+PHNP+G+ +  A   ALA++    D+ ++SDEVY  +++
Sbjct: 151 IPWDKVKAAVTPKTRMIMVNTPHNPTGSVMRAADVAALADIVRGTDILILSDEVYEHMVY 210

Query: 213 DGE-HVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGSP 271
           DG+ H S A  P +A+R+   +S  K++ +TGW+VG+V  PAAL A    +    ++   
Sbjct: 211 DGQPHESLARHPELAERSFINSSFGKTYHVTGWKVGYVAAPAALTAEFRKVHQFNVFTVN 270

Query: 272 EFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVDIRP- 330
             +Q      ++ P P L+ +   Y+ +RDL    LA++     L   G  F  V     
Sbjct: 271 TPVQYGLAAYMKDPAPYLD-LPAFYQHKRDLFRTGLANT-RFELLPSQGTYFQCVKYGAI 328

Query: 331 TGLSAQAFADRLLDRHGVSVLAGEAF--GPSAAGHIRLGLVLGAEPLREACRRIA 383
           + L    F   L    GV+ +   AF   P  +G +R       E L+ A  R+A
Sbjct: 329 SALPEAEFCKWLTSEIGVAAIPVSAFYNTPRESGIVRFCFAKKDETLQLALERLA 383


Lambda     K      H
   0.322    0.136    0.411 

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: 348
Number of extensions: 13
Number of successful extensions: 4
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: 393
Length of database: 385
Length adjustment: 30
Effective length of query: 363
Effective length of database: 355
Effective search space:   128865
Effective search space used:   128865
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 (21.9 bits)
S2: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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