GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astB in Caulobacter crescentus NA1000

Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate CCNA_01680 CCNA_01680 succinylarginine dihydrolase

Query= reanno::SB2B:6937151
         (444 letters)



>FitnessBrowser__Caulo:CCNA_01680
          Length = 446

 Score =  416 bits (1068), Expect = e-120
 Identities = 223/445 (50%), Positives = 287/445 (64%), Gaps = 9/445 (2%)

Query: 4   FEANFDGLVGPTHNYAGLSFGNVASQSNAAQVSNPKDAAKQGLKKAKALADMGMVQGMLA 63
           FEAN DGLVGPTH+Y GLS GN+AS  NA +VSNP+ AA +GL K + LAD+G+ Q +L 
Sbjct: 5   FEANCDGLVGPTHSYVGLSPGNLASTRNAGEVSNPRGAALEGLAKMRRLADLGLPQFVLP 64

Query: 64  PQERPDIHTLRRVGFTGSDADVLSQAAKASPVLLQACASASSMWTANAATVSPSADSDDG 123
           P ERP +  LR++GF+G D  VL+ A + +P L  A  SAS MW ANAATV+PSAD+ DG
Sbjct: 65  PHERPAVSLLRQLGFSGPDEIVLTSAWRDAPALAAAACSASPMWAANAATVTPSADAADG 124

Query: 124 KLHFTPANLVDKLHRSIEPVTTGNILKAIFTDERYFAHHQHLPEHPHFGDEGAANHTRLC 183
           ++HFTPANL+  LHRS+E   T   L+ +F DE  FA H  LP  PHF DEGAANH RLC
Sbjct: 125 RVHFTPANLLTNLHRSLEGRQTARSLRRLFADETRFAVHDPLPAQPHFADEGAANHVRLC 184

Query: 184 HDYGQAGVEVFVYGRSVADLSRPAPVKYPARQTLEASQAVARLHQLSDDRTVYMQQNPDV 243
            ++G  GV +FV+GR   +       ++PARQT EA +A+ R H  +  R V+ QQ    
Sbjct: 185 AEHGGPGVNLFVWGR---EAWSHWDGRFPARQTKEAFEAIQRRHGAA--RAVFPQQGKAA 239

Query: 244 IDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEIDKKMHG--NMYFIEVPTAKVSVQD 301
           I+ G FHNDV+ VG +  LF+HE+AF +      E+     G     F+EV  A + + D
Sbjct: 240 IEGGAFHNDVVCVGTRECLFFHERAFEDRATMAREVRAAASGLFEPAFVEVTEADLPMAD 299

Query: 302 AVKSYLFNTQIITL-SDGNMAIIAPTDCQENPAVHAYLNELVTLNTPIKAVHYFDVKQSM 360
            V SYLFN+Q++ +  +  + ++AP + ++NP  +A    L T N PI  V Y DV+QSM
Sbjct: 300 LVASYLFNSQLLVVPGEDRLVLLAPVETRDNPRAYAVAESLATSNGPIGRVEYVDVRQSM 359

Query: 361 QNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADPQLL 420
           +NGGGPACLRLRV + E ELAA NP       L   L  W+ + YRDRLS  DLAD +LL
Sbjct: 360 RNGGGPACLRLRVVLTEAELAAANPAQRFTADLQDALADWITRRYRDRLSPADLADAKLL 419

Query: 421 MESRTALDELTQIMKLG-SVYQFQR 444
            ESR ALDELTQI+ LG   Y FQR
Sbjct: 420 TESREALDELTQILGLGDDFYPFQR 444


Lambda     K      H
   0.318    0.131    0.380 

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: 496
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: 444
Length of database: 446
Length adjustment: 32
Effective length of query: 412
Effective length of database: 414
Effective search space:   170568
Effective search space used:   170568
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 CCNA_01680 CCNA_01680 (succinylarginine dihydrolase)
to HMM TIGR03241 (astB: succinylarginine dihydrolase (EC 3.5.3.23))

Software error:

../bin/blast/fastacmd -i /tmp/list.30547.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30547.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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