GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Desulfovibrio vulgaris Miyazaki F

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= BRENDA::Q9K9B2
         (515 letters)



>FitnessBrowser__Miya:8501416
          Length = 1013

 Score =  477 bits (1228), Expect = e-139
 Identities = 236/512 (46%), Positives = 324/512 (63%)

Query: 2   LQPYKHEPFTDFTVEANRKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKD 61
           L P+ +E   D T+ ANR  F  A+  V  + G   PL I G+ VTT+D I S NPA+  
Sbjct: 484 LPPFVNESMLDLTIPANRAGFVNAIAEVRGKAGGVIPLFIGGKDVTTDDTIASTNPAKPA 543

Query: 62  QLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVH 121
           +++  V +  +   + AI++A +AF  WR+ +P +RA  L +AA I RRR  E SAW V 
Sbjct: 544 EVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAMFLHRAADIARRRMFELSAWQVL 603

Query: 122 EAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPW 181
           E GK W +A  D  E IDFL+YYA +M+ L   + +   PGE N  FY P G+   I+PW
Sbjct: 604 EVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPRRMGRAPGELNHLFYQPKGIAAVIAPW 663

Query: 182 NFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEV 241
           NF  AI +G A A IVTGN V+ KP+S    +     E+  +AGLP+GV NYVPG  + +
Sbjct: 664 NFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTEIFREAGLPEGVFNYVPGRSSVM 723

Query: 242 GDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADL 301
           GDYLV+HP+ S+I FTGS +VG+R+ E+AA V+PGQ   KRVI EMGGK+ +++D DADL
Sbjct: 724 GDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQCKRVIAEMGGKNAIIIDDDADL 783

Query: 302 DLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGP 361
           D A   +L SAFGF GQKCSA SR ++   +YD  +E+ V  A+ + +G   +  NYMGP
Sbjct: 784 DEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVERLVKAAQAIKIGPSEDPANYMGP 843

Query: 362 VIDEKAFEKIMSYIEIGKKEGRLMTGGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPV 421
           V D    + I+ Y+++ ++EG+++       + G ++  TI+  + P   I QEEIFGPV
Sbjct: 844 VADASLQKNILEYVKVAEQEGKVLVKRTDIPAEGCYVPLTIVEGIKPHHRIAQEEIFGPV 903

Query: 422 VAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGY 481
           +A  +A +FD AL IAN T + LTG V +R+  ++ +A+REF VGNLY NR  TGA+V  
Sbjct: 904 LAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLTKARREFRVGNLYLNRGSTGAMVER 963

Query: 482 HPFGGFKMSGTDSKAGGPDYLALHMQAKTVSE 513
            PFGGFKMSG  SK GGPDYL   M  + V+E
Sbjct: 964 QPFGGFKMSGVGSKTGGPDYLLQFMDPRCVTE 995


Lambda     K      H
   0.316    0.134    0.388 

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: 1189
Number of extensions: 50
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: 515
Length of database: 1013
Length adjustment: 40
Effective length of query: 475
Effective length of database: 973
Effective search space:   462175
Effective search space used:   462175
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: 55 (25.8 bits)

Align candidate 8501416 DvMF_2146 (delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq))
to HMM TIGR01237 (pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

Software error:

../bin/blast/fastacmd -i /tmp/list.32752.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32752.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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