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_RS10805 HSERO_RS10805 succinyldiaminopimelate aminotransferase

Query= BRENDA::Q9HUI9
         (393 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS10805 HSERO_RS10805
           succinyldiaminopimelate aminotransferase
          Length = 403

 Score =  105 bits (263), Expect = 2e-27
 Identities = 112/377 (29%), Positives = 170/377 (45%), Gaps = 27/377 (7%)

Query: 37  LSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSG--QAVDAEQ 94
           L +G+P   TPA I QA ID+L AG   Y    G  ALR  IA+  ++R    +   A +
Sbjct: 34  LGIGEPKHPTPAFIQQALIDNL-AGLASYPATLGSDALRGAIADWLQKRYDIPRPDPATE 92

Query: 95  VVVLAGAQCALYAVVQCLLNP---GDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENGF 151
           ++ + G++ AL+++ Q +++P   G  V+   P Y  YE      GA+   V    +  F
Sbjct: 93  ILPVNGSREALFSLTQTVVDPTRPGALVMCPNPFYQIYEGSAYLAGAQPYFVNSDPKRNF 152

Query: 152 RVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELL 211
                +V   +  R + + + SP NP+GA L    W+ L  L   +   + SDE YSE+ 
Sbjct: 153 APDFSQVPQDVWERVQLLFVCSPGNPTGAVLTLEDWKELFALSDRYGFVIASDECYSEIY 212

Query: 212 FDGE----HVSPASLPGM-ADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCM 266
           F+ +     +  A L G    R  + +SLSK   + G R G+V G AA+   L+   L  
Sbjct: 213 FNEDPPLGGMQAARLLGRDYRRLISFSSLSKRSNVPGMRSGFVAGDAAI---LKKFLLYR 269

Query: 267 LY---GSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMF 323
            Y        IQ A+  A +     ++     Y  +   V   L +   L    PD   +
Sbjct: 270 TYHGAAMSPVIQAASVLAWQDE-THVQGNIAKYVTKFSQVTPLLQEV--LEVALPDAAFY 326

Query: 324 VMVDI-RPTGLSAQAFADRLLDRHGVSVLAG-----EAFGPS-AAGHIRLGLVLGAEPLR 376
           +   + +   +S   FA RL   + V+VL G     EA G +  AG IR+ LV   E   
Sbjct: 327 LWAKVDKLVNISDTEFAQRLYAEYNVTVLPGSYLAREAHGVNPGAGRIRMALVAEVEECL 386

Query: 377 EACRRIALCAAELLGQA 393
           EA +RI     +L GQA
Sbjct: 387 EAAQRIVAFTRKLAGQA 403


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: 423
Number of extensions: 23
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: 393
Length of database: 403
Length adjustment: 31
Effective length of query: 362
Effective length of database: 372
Effective search space:   134664
Effective search space used:   134664
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