GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argH in Dinoroseobacter shibae DFL-12

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate 3609679 Dshi_3062 argininosuccinate lyase (RefSeq)

Query= BRENDA::Q8DVX5
         (460 letters)



>FitnessBrowser__Dino:3609679
          Length = 463

 Score =  438 bits (1127), Expect = e-127
 Identities = 232/459 (50%), Positives = 301/459 (65%), Gaps = 1/459 (0%)

Query: 3   TKNHKLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAAT 62
           TK++ +WGGRF AG    +E   ASI FD++LA  D+ GS AH  ML ++GI+S +DA  
Sbjct: 4   TKSNAMWGGRFAAGPDAIMEAINASIGFDRRLARQDIDGSRAHAAMLAQQGILSSKDAEA 63

Query: 63  IKAGLEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMH 122
           I+ GL  +L E + GQ  F  + EDIHMN+E+ L   IG  AG+LHT RSRNDQVATD  
Sbjct: 64  IREGLLTVLSEIETGQFAFSAALEDIHMNVEARLKELIGEPAGRLHTGRSRNDQVATDFK 123

Query: 123 LYLKAKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTR 182
           L+++ +LD     L  L   L+  A+     +MPG+THLQ AQP+++GHH+MAY  MF R
Sbjct: 124 LWVRDQLDAADAGLLALLRALLAQAEAGADWVMPGFTHLQTAQPVTWGHHMMAYVEMFAR 183

Query: 183 DSERFIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEF 242
           D  R        +  PLGAAALAGT+FP+DR+ TAQ +GF  P +NSLDAVSDRDF LEF
Sbjct: 184 DRGRMQDARARMNECPLGAAALAGTSFPLDRDATAQALGFDRPAANSLDAVSDRDFALEF 243

Query: 243 LSNASILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGR 302
           L+ ASI  MH+SRM EE++ W S +++FVTLSD FSTGSSIMPQKKNPD AELIR K GR
Sbjct: 244 LAAASICAMHLSRMAEELVIWSSAQFRFVTLSDRFSTGSSIMPQKKNPDAAELIRAKIGR 303

Query: 303 VYANLFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAE 362
           +      LLTVMK LPLAY+KD+QEDKE +FD A+T+ +AL  + GM+  M  N   + +
Sbjct: 304 IVGANVALLTVMKGLPLAYSKDMQEDKEQVFDAADTLMLALAAMEGMVRDMTANRASLED 363

Query: 363 STQKDFSNATELADYLASK-GMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLI 421
           +    FS AT+LAD+L  +  +PFR AH + G L+      G  L D+ L   Q++   I
Sbjct: 364 AAASGFSTATDLADWLVRELNLPFRDAHHVTGTLVAMAEAKGCDLPDLSLAEMQSVHGAI 423

Query: 422 EEDVYETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460
             DV+E L  H +V  R S GGT   QV+ Q+A  K+ L
Sbjct: 424 RADVFEVLGVHNSVASRTSYGGTAPSQVRAQVARWKERL 462


Lambda     K      H
   0.318    0.132    0.378 

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: 558
Number of extensions: 20
Number of successful extensions: 3
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: 460
Length of database: 463
Length adjustment: 33
Effective length of query: 427
Effective length of database: 430
Effective search space:   183610
Effective search space used:   183610
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 3609679 Dshi_3062 (argininosuccinate lyase (RefSeq))
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.4702.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4702.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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