GapMind for Amino acid biosynthesis

 

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

Align amino-acid acetyltransferase (characterized)
to candidate 5211062 Shew_3478 N-acetylglutamate synthase (RefSeq)

Query= CharProtDB::CH_024150
         (443 letters)



>FitnessBrowser__PV4:5211062
          Length = 440

 Score =  584 bits (1506), Expect = e-171
 Identities = 280/438 (63%), Positives = 351/438 (80%)

Query: 5   RKTELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLVVVYG 64
           R TELVEGFRHS  Y+N HRGKTFV+MLGGEA+    F SI+NDI LLHSLGI++V+V+G
Sbjct: 2   RTTELVEGFRHSASYVNAHRGKTFVVMLGGEALAQSQFRSIINDIALLHSLGIKIVLVHG 61

Query: 65  ARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTPLQGA 124
           ARPQID  LAAH+  P Y+  +R++D ++  ++KQ  G LQLDITARLSMSL+NTP+QGA
Sbjct: 62  ARPQIDEALAAHNLAPEYYNGVRISDEESFRVIKQVVGGLQLDITARLSMSLSNTPMQGA 121

Query: 125 HINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSVTGES 184
            INVVSGNF+IAQPLGVD+GVDYC SG++RRID   + RQLD+  IVL+GPVA SVTGE 
Sbjct: 122 QINVVSGNFVIAQPLGVDNGVDYCLSGKVRRIDVAGLRRQLDNHGIVLLGPVAASVTGEC 181

Query: 185 FNLTSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEKGDYN 244
           FNLT+EE+ATQ+A+KLKA+KMIGF + +G+ + +G++++EL P +AQ  +    ++ ++ 
Sbjct: 182 FNLTAEEVATQIAVKLKADKMIGFSAKEGILDSNGEVIAELMPTDAQRILSELTDEDNWC 241

Query: 245 SGTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRRATIN 304
            GT  FL+ ++ ACR+GV RCH +SY +DGALLQELFSRDGIGTQIV ESAE++RRATI 
Sbjct: 242 VGTRAFLQASIDACRNGVARCHFVSYLDDGALLQELFSRDGIGTQIVTESAERLRRATIA 301

Query: 305 DIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKIGEMA 364
           DIGG+L+LIRPLEQ G+LVRRSREQLEMEI++F +I+RD   I CAALYPF E+  GE A
Sbjct: 302 DIGGVLDLIRPLEQAGVLVRRSREQLEMEIEQFMLIERDGLVIGCAALYPFEEDNAGEFA 361

Query: 365 CVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDLLPES 424
           C+ VHPDYR + RG +LL+ I  QAK  G ++LF LTTRSIHWF E GF  V++D LP  
Sbjct: 362 CLVVHPDYRDADRGSILLKNIIGQAKVRGYARLFALTTRSIHWFLEHGFQIVEVDALPNK 421

Query: 425 KKQLYNYQRKSKVLMADL 442
           KKQLYNYQRKSK+L  DL
Sbjct: 422 KKQLYNYQRKSKILALDL 439


Lambda     K      H
   0.319    0.136    0.384 

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: 594
Number of extensions: 12
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: 443
Length of database: 440
Length adjustment: 32
Effective length of query: 411
Effective length of database: 408
Effective search space:   167688
Effective search space used:   167688
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate 5211062 Shew_3478 (N-acetylglutamate synthase (RefSeq))
to HMM TIGR01890 (argA: amino-acid N-acetyltransferase (EC 2.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.8561.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8561.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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