GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astE in Pseudomonas fluorescens FW300-N2E2

Align Succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate Pf6N2E2_5671 Succinylglutamate desuccinylase (EC 3.5.1.96)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1977
         (336 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5671
          Length = 335

 Score =  602 bits (1552), Expect = e-177
 Identities = 305/336 (90%), Positives = 320/336 (95%), Gaps = 1/336 (0%)

Query: 1   MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG 60
           MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEV+PPEARDNGLDLLLSAGIHG
Sbjct: 1   MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVKPPEARDNGLDLLLSAGIHG 60

Query: 61  NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS 120
           NETAPIELLDRLLHDIARG LKPRARILFLFGNPEAIR+GERFVEQDVNRLFNGRHE S 
Sbjct: 61  NETAPIELLDRLLHDIARGHLKPRARILFLFGNPEAIRRGERFVEQDVNRLFNGRHELSG 120

Query: 121 GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR 180
           G EALRACELERLAASFFS P+R RLHYDLHTAIRGSKIEQFALYPWKE RQHSR+ELAR
Sbjct: 121 GPEALRACELERLAASFFSRPERSRLHYDLHTAIRGSKIEQFALYPWKEGRQHSRRELAR 180

Query: 181 LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI 240
           LRA GMEAVLLQNKPSIVFS+YTYD+LGAE+FTLELGKARPFGQNDGVNVSLLE RL+QI
Sbjct: 181 LRAGGMEAVLLQNKPSIVFSAYTYDQLGAESFTLELGKARPFGQNDGVNVSLLETRLQQI 240

Query: 241 IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR 300
           IEG EPEL ++ LDGLQL+SVAREIIKHSDSFRLNLPADIENFSEL  GY+LAEDIA TR
Sbjct: 241 IEGNEPEL-DEGLDGLQLFSVAREIIKHSDSFRLNLPADIENFSELGKGYVLAEDIAQTR 299

Query: 301 WIIEEEGARIIFPNPRVKNGLRAGILVVPTTDENLA 336
           W+IEEEGARIIFPNP+VKNGLRAGIL+VP TDENLA
Sbjct: 300 WVIEEEGARIIFPNPKVKNGLRAGILIVPATDENLA 335


Lambda     K      H
   0.319    0.138    0.394 

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: 507
Number of extensions: 19
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: 336
Length of database: 335
Length adjustment: 28
Effective length of query: 308
Effective length of database: 307
Effective search space:    94556
Effective search space used:    94556
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: 49 (23.5 bits)

Align candidate Pf6N2E2_5671 (Succinylglutamate desuccinylase (EC 3.5.1.96))
to HMM TIGR03242 (astE: succinylglutamate desuccinylase (EC 3.5.1.96))

Software error:

../bin/blast/fastacmd -i /tmp/list.11719.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11719.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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