GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argG in Phaeobacter inhibens BS107

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate GFF3439 PGA1_c34920 argininosuccinate synthase ArgG

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__Phaeo:GFF3439
          Length = 408

 Score =  491 bits (1263), Expect = e-143
 Identities = 246/399 (61%), Positives = 300/399 (75%), Gaps = 5/399 (1%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGAS--KAIAL 59
           K+VLAYSGGLDTSIILKWL+  Y  EV+ FTAD+GQGEE+E AR+KA   G         
Sbjct: 6   KVVLAYSGGLDTSIILKWLQTEYGCEVVTFTADLGQGEELEPARQKAELLGIKPENIFIE 65

Query: 60  DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119
           D++EEFVRDFVFPM RA AVYEG YLLGTSIARPLI+K LV IAE  GA+A+AHGATGKG
Sbjct: 66  DVREEFVRDFVFPMFRANAVYEGLYLLGTSIARPLISKRLVEIAEATGADAVAHGATGKG 125

Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQ--EKPYSMDAN 177
           NDQVRFEL AYAL PDIKVIAPWREW    R  ++ +AEAH IPV   +  E P+S+DAN
Sbjct: 126 NDQVRFELAAYALNPDIKVIAPWREWDLTSRTRLLEFAEAHQIPVAKDKRGEAPFSVDAN 185

Query: 178 LLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAA 237
           LLH S EG VLEDP    P  +++ T  PE+AP+  E++E+ F +GD V++NGE +SPA 
Sbjct: 186 LLHTSSEGKVLEDPAVAAPDYVYQRTVHPEDAPNEAEFIEIGFEKGDAVSINGEAMSPAT 245

Query: 238 LLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQ 297
           +L +LNE GG+HG+GR+D+VE RFVGMKSRG+YETPGGTIL  A R +ES+T+DR  +H 
Sbjct: 246 ILTQLNEYGGKHGIGRLDLVEGRFVGMKSRGIYETPGGTILLEAHRGIESITMDRGAMHL 305

Query: 298 RDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSL 357
           +D L P+YAEL+Y GFWY+PERE LQA  D     VTG  R+KLYKG+   VGR +  SL
Sbjct: 306 KDQLMPQYAELIYNGFWYSPEREMLQAAIDRSQEHVTGTVRVKLYKGSATTVGRWSDHSL 365

Query: 358 YRQDLVSF-DEAGGYDQKDAEGFIKIQALRLRVRALVER 395
           Y +  V+F D+AG YDQKDA GFI++ ALRL++ A  ER
Sbjct: 366 YSEAHVTFEDDAGAYDQKDAAGFIQLNALRLKLLAARER 404


Lambda     K      H
   0.319    0.137    0.402 

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: 514
Number of extensions: 18
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: 400
Length of database: 408
Length adjustment: 31
Effective length of query: 369
Effective length of database: 377
Effective search space:   139113
Effective search space used:   139113
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: 50 (23.9 bits)

Align candidate GFF3439 PGA1_c34920 (argininosuccinate synthase ArgG)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.22863.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.22863.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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