GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Echinicola vietnamensis KMM 6221, DSM 17526

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Echvi_1300 Echvi_1300 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1

Query= BRENDA::P30038
         (563 letters)



>FitnessBrowser__Cola:Echvi_1300
          Length = 543

 Score =  513 bits (1321), Expect = e-150
 Identities = 258/530 (48%), Positives = 351/530 (66%), Gaps = 3/530 (0%)

Query: 34  NEPVLAFTQGSPERDALQKALKDLKGRMEAIPCVVGDEEVWTSDVQYQVSPFNHGHKVAK 93
           NEPV  +  G+P R  LQ AL++ + +   +P  +G EEV T +      P +H H +  
Sbjct: 13  NEPVFDYAPGTPARAKLQAALQEARSKEVDVPMYIGSEEVRTGNKIPLSPPHDHQHLLGH 72

Query: 94  FCYADKSLLNKAIEAALAARKEWDLKPIADRAQIFLKAADMLSGPRRAEILAKTMVGQGK 153
           F   DKS + +AI AAL A++ W+      RA IFLKAAD+++GP R ++ A TM+GQ K
Sbjct: 73  FHEGDKSHVEQAINAALGAKEAWETMEWEQRAAIFLKAADLIAGPYRYKMNAATMLGQSK 132

Query: 154 TVIQAEIDAAAELIDFFRFNAKYAVELEGQQP-ISVPPSTNSTVYRGLEGFVAAISPFNF 212
              QAEID+A E++DF RFN KY  E+  QQP IS     N    R LEGFV A++PFNF
Sbjct: 133 NAFQAEIDSACEIVDFLRFNVKYMTEIYKQQPPISGDGVWNRLEQRPLEGFVFALTPFNF 192

Query: 213 TAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPLFGDT 272
           TAI GNL  APA+MGN V+WKP+ T +  +  + ++ REAG+P  +I  V  DGP  G+ 
Sbjct: 193 TAIAGNLPTAPAMMGNTVVWKPAYTQIYTANLLMQVFREAGVPDGVINLVYVDGPAAGEV 252

Query: 273 VTSSEHLCGINFTGSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKNFHFVHRSADVESV 332
           +       GI+FTGS   F+ +WK +  N++++ ++PR+ GE GGK+F   H+SAD + +
Sbjct: 253 IFEHPEFAGIHFTGSTAVFQTIWKTIGNNIEKYKSYPRIVGETGGKDFVIAHKSADAKQL 312

Query: 333 VSGTLRSAFEYGGQKCSACSRLYVPHSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVI 392
            +G +R AFE+ GQKCSA SR Y+P +LW  +K  + E+ + IK+G P EDF  F +AVI
Sbjct: 313 ATGLVRGAFEFQGQKCSAASRAYIPSNLWEDVKKYMQEDLASIKMGGP-EDFSNFINAVI 371

Query: 393 DAKSFARIKKWLEHARSSPSLTILAGGKCDDSVGYFVEPCIVESKDPQEPIMKEEIFGPV 452
           D KSF +I K+++ A+S   L ++AGG  D S GYFVEP ++ +KDP    M EEIFGPV
Sbjct: 372 DEKSFDKIAKYIDTAKSD-GLEVVAGGHYDKSKGYFVEPTVLLTKDPMYTTMCEEIFGPV 430

Query: 453 LSVYVYPDDKYKETLQLVDSTTSYGLTGAVFSQDKDVVQEATKVLRNAAGNFYINDKSTG 512
           L++YVY +D ++E L+LVD T+ YGLTGA+FS D+   Q AT+ LRNAAGNFYINDK TG
Sbjct: 431 LTIYVYQEDHFEEALELVDQTSPYGLTGAIFSHDRYAAQLATQKLRNAAGNFYINDKPTG 490

Query: 513 SIVGQQPFGGARASGTNDKPGGPHYILRWTSPQVIKETHKPLGDWSYAYM 562
           ++VGQQPFGGAR SGTNDK G    +LRW SP+ IKET     D+ Y ++
Sbjct: 491 AVVGQQPFGGARKSGTNDKAGAMINMLRWVSPRTIKETFVTPTDYRYPFL 540


Lambda     K      H
   0.319    0.135    0.411 

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: 870
Number of extensions: 37
Number of successful extensions: 4
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: 563
Length of database: 543
Length adjustment: 36
Effective length of query: 527
Effective length of database: 507
Effective search space:   267189
Effective search space used:   267189
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: 53 (25.0 bits)

Align candidate Echvi_1300 Echvi_1300 (delta-1-pyrroline-5-carboxylate dehydrogenase, group 1)
to HMM TIGR01236 (pruA: 1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

Software error:

../bin/blast/fastacmd -i /tmp/list.10807.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10807.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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