GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutI in Shewanella amazonensis SB2B

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate 6935865 Sama_0080 imidazolonepropionase (RefSeq)

Query= reanno::MR1:199292
         (408 letters)



>FitnessBrowser__SB2B:6935865
          Length = 412

 Score =  685 bits (1768), Expect = 0.0
 Identities = 335/412 (81%), Positives = 374/412 (90%), Gaps = 4/412 (0%)

Query: 1   MSWDQVWIDVNVATMDPSISAPYGAITHAAIAVKDGKIAWLGPRSELPAFDVLSIPVYRG 60
           MSWDQVWID+N+ATMDPS++  YGAIT AA+AVKDGKIAWLG RS+LP FDVL+ PV+RG
Sbjct: 1   MSWDQVWIDINIATMDPSMNEAYGAITDAALAVKDGKIAWLGKRSDLPEFDVLATPVHRG 60

Query: 61  KGGWITPGLIDAHTHLVFAGNRANEFELRLKGATYEEIARAGGGIISTVNACREADEAAL 120
            GGW+TPGLIDAHTHLVFAGNRANEFELRL+GA+YEEIARAGGGI+STV ACR+ADEA L
Sbjct: 61  HGGWLTPGLIDAHTHLVFAGNRANEFELRLQGASYEEIARAGGGIVSTVKACRDADEAEL 120

Query: 121 FELGRQRLNALAKEGVTTVEIKSGYGLDTETELKILRVARELGKHHHVDVKTTFLGAHAV 180
           F+L R+RLNALAKEGVTTVEIKSGYGLD +TELK+LRVARELG+HHHVDV TTFLGAHAV
Sbjct: 121 FDLARRRLNALAKEGVTTVEIKSGYGLDLDTELKLLRVARELGQHHHVDVVTTFLGAHAV 180

Query: 181 PPEYK----GNSDGYVDLIINKMLPAVIKENLADAVDVFCENIAFNLEQTERVLSAAKAA 236
           PPE+K      +D YVDL++N+MLPAV+ ENLADA DVFCENIAFNLEQTERVLSAAK  
Sbjct: 181 PPEFKTLGEAGTDAYVDLVVNEMLPAVVAENLADAADVFCENIAFNLEQTERVLSAAKTL 240

Query: 237 GLQVKLHAEQLSNMGGSELAARLGAKSVDHIEYLDEAGVKALSESGTCAVLLPGAFYFLR 296
           GL +KLHAEQLSN+GGSELAARLGAKSVDHIEYLDEAGVKA+++SGTCAVLLPGAFYFLR
Sbjct: 241 GLDIKLHAEQLSNLGGSELAARLGAKSVDHIEYLDEAGVKAIAQSGTCAVLLPGAFYFLR 300

Query: 297 ETQKPPIDLLRQYGVPMVLASDFNPGSFPICSTLLMLNMGCTLFRLTPEEALAGLTLNAA 356
           ET+ PPIDLLRQY VPMVLASDFNPGS PICSTLLMLNMGCTLFRLTPEEALAG+T NAA
Sbjct: 301 ETKLPPIDLLRQYQVPMVLASDFNPGSSPICSTLLMLNMGCTLFRLTPEEALAGVTRNAA 360

Query: 357 KALGIEDKVGSLVVGKQADFCLWNIATPAQLAYSYGVNPCKDVVKNGKLVHQ 408
           +ALG + +VG L  G +ADFCLW I+TPA+LAYSYGVNP  DVVK G+L+HQ
Sbjct: 361 RALGRDQRVGVLREGMEADFCLWRISTPAELAYSYGVNPLVDVVKGGRLIHQ 412


Lambda     K      H
   0.319    0.136    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: 633
Number of extensions: 14
Number of successful extensions: 2
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: 408
Length of database: 412
Length adjustment: 31
Effective length of query: 377
Effective length of database: 381
Effective search space:   143637
Effective search space used:   143637
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 6935865 Sama_0080 (imidazolonepropionase (RefSeq))
to HMM TIGR01224 (hutI: imidazolonepropionase (EC 3.5.2.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.4869.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4869.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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