GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argH in Shewanella loihica PV-4

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate 5207684 Shew_0206 argininosuccinate lyase (RefSeq)

Query= ecocyc::ARGSUCCINLYA-MONOMER
         (457 letters)



>FitnessBrowser__PV4:5207684
          Length = 453

 Score =  602 bits (1551), Expect = e-176
 Identities = 308/450 (68%), Positives = 352/450 (78%)

Query: 1   MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEE 60
           MALWGGRF+Q +   FK FNDSL  DYRL E+DIVGS+AW+ A+  VG+L+ +E   L++
Sbjct: 1   MALWGGRFSQESSALFKLFNDSLPVDYRLVEEDIVGSIAWADAITGVGILSQQECQSLKQ 60

Query: 61  ALNVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW 120
           AL  LL +V+ +P+ IL S AED HS+VE  LI KVG LGKKLHTGRSRNDQVATDLKLW
Sbjct: 61  ALQELLAEVKDQPETILASGAEDTHSFVEQALIAKVGDLGKKLHTGRSRNDQVATDLKLW 120

Query: 121 CKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE 180
           CK     LL    QL++AL+  A+   DAVMPGYTHLQRAQPV F HWCLAYVEM  RD 
Sbjct: 121 CKKEGKALLELLAQLKAALLSLAERELDAVMPGYTHLQRAQPVAFGHWCLAYVEMFERDI 180

Query: 181 SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS 240
           SRLQD L+RLD  PLG GALAGTAY +DR  LA  LGFAS T NSLDSVSDRDHV+EL S
Sbjct: 181 SRLQDCLQRLDTCPLGTGALAGTAYPMDRYALAKSLGFASPTLNSLDSVSDRDHVIELCS 240

Query: 241 AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ 300
            AAI M+HLSR AEDLIFFN+GEAGF+EL D+VTSGSSLMPQKKNPDALELIRGK GRV 
Sbjct: 241 DAAISMMHLSRMAEDLIFFNSGEAGFIELDDQVTSGSSLMPQKKNPDALELIRGKTGRVY 300

Query: 301 GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAA 360
           G+L G++ T+K LPLAYNKDMQEDKEGLFD +D+W  CL MAALVL G++V R     AA
Sbjct: 301 GSLMGILTTMKALPLAYNKDMQEDKEGLFDVMDSWSICLEMAALVLSGLKVNRENTLSAA 360

Query: 361 QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDED 420
           QQGYANATELADYLVAKG+PFREAHH+VGE VVEAI Q KP+E+  L+ LQ F+ VI ED
Sbjct: 361 QQGYANATELADYLVAKGMPFREAHHVVGEVVVEAIAQKKPIEEFELASLQVFASVIQED 420

Query: 421 VYPILSLQSCLDKRAAKGGVSPQQVAQAIA 450
           VY  L++ SCL KR A GG S  QV  A+A
Sbjct: 421 VYQCLTIDSCLAKREALGGTSLTQVKAALA 450


Lambda     K      H
   0.318    0.133    0.386 

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: 570
Number of extensions: 15
Number of successful extensions: 1
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: 457
Length of database: 453
Length adjustment: 33
Effective length of query: 424
Effective length of database: 420
Effective search space:   178080
Effective search space used:   178080
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: 51 (24.3 bits)

Align candidate 5207684 Shew_0206 (argininosuccinate lyase (RefSeq))
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.31771.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31771.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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