GapMind for catabolism of small carbon sources

 

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

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate 5208068 Shew_0580 succinylglutamic semialdehyde dehydrogenase (RefSeq)

Query= reanno::MR1:199807
         (487 letters)



>FitnessBrowser__PV4:5208068
          Length = 487

 Score =  857 bits (2215), Expect = 0.0
 Identities = 418/486 (86%), Positives = 451/486 (92%)

Query: 1   MTHFIKGQWHTGKGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDA 60
           M+ FI GQW  G GHDV S NPAN E+IW  +TAT EQVNAAV+AAR AQFDWF+LGFDA
Sbjct: 2   MSQFINGQWVAGLGHDVVSKNPANQEVIWESKTATPEQVNAAVEAARAAQFDWFMLGFDA 61

Query: 61  RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYNKRTGTET 120
           RL IVEAYR QLEA+K ++AE IAQETGKPQWETATE  AMIGKIGLS +AY+KRTGT  
Sbjct: 62  RLAIVEAYRDQLEAHKGDIAEVIAQETGKPQWETATEAGAMIGKIGLSVAAYHKRTGTSE 121

Query: 121 NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVFKPSELTPKVAELM 180
           NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGN+VVFKPSELTPK AELM
Sbjct: 122 NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKTAELM 181

Query: 181 VTLWEKSGLPAGVLNLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240
           + LWEK+GLPAGV+NLVQGEV+TGKALASHPQ+DGLFFTGSSRTGH+LHQQYAGHPGKIL
Sbjct: 182 LKLWEKAGLPAGVINLVQGEVETGKALASHPQIDGLFFTGSSRTGHILHQQYAGHPGKIL 241

Query: 241 ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE 300
           ALEMGGNNPLIIKGV D  AAVHDI+QSAYISSGQRCTCARRLYVE+G +GDAL+AKL E
Sbjct: 242 ALEMGGNNPLIIKGVKDTLAAVHDIIQSAYISSGQRCTCARRLYVEKGAEGDALLAKLAE 301

Query: 301 AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLLSLGGVPLVELMHLQAGTGLVSP 360
           AVKQIKVGPWNAQPQPFMGSMISEAAAKGMV AQ NL++LGG PLVEL HL+AGTGLVSP
Sbjct: 302 AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVEAQRNLINLGGTPLVELKHLEAGTGLVSP 361

Query: 361 GLIDVTAVSELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSREDYEYFLA 420
           GLIDVT V ELPDEEYFGPLLQ+VRY+DFD+AIKLAN TRYGLSAGILADSREDY+YFLA
Sbjct: 362 GLIDVTQVIELPDEEYFGPLLQVVRYTDFDEAIKLANDTRYGLSAGILADSREDYDYFLA 421

Query: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPATL 480
           RIRAGIVNWNKQITGASG+APFGGVGASGNHRASAFYAADYCAYPVASVEADA+++PA+L
Sbjct: 422 RIRAGIVNWNKQITGASGSAPFGGVGASGNHRASAFYAADYCAYPVASVEADALAMPASL 481

Query: 481 SPGLTL 486
           SPGLTL
Sbjct: 482 SPGLTL 487


Lambda     K      H
   0.316    0.133    0.391 

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: 985
Number of extensions: 29
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: 487
Length of database: 487
Length adjustment: 34
Effective length of query: 453
Effective length of database: 453
Effective search space:   205209
Effective search space used:   205209
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate 5208068 Shew_0580 (succinylglutamic semialdehyde dehydrogenase (RefSeq))
to HMM TIGR03240 (astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71))

Software error:

../bin/blast/fastacmd -i /tmp/list.21160.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21160.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.