GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Caulobacter crescentus NA1000

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate CCNA_03206 CCNA_03206 L-serine dehydratase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4954
         (458 letters)



>FitnessBrowser__Caulo:CCNA_03206
          Length = 462

 Score =  488 bits (1256), Expect = e-142
 Identities = 257/464 (55%), Positives = 335/464 (72%), Gaps = 8/464 (1%)

Query: 1   MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALVDHGFLADVRRVEIRLYGSLSATGVG 60
           M  SVFDLFK+G+GPSSSHT+GPM AA  F   L D G LA V RVE RLY SL+ TG G
Sbjct: 1   MTASVFDLFKLGVGPSSSHTMGPMTAAVLFIGRLRDAGKLAAVARVETRLYASLALTGRG 60

Query: 61  HATDRACVMGLMGEWPDRIDPTTIDSRIHTLRETGKLCLAGVAQIAFDWQRDLLLLD-ES 119
           HATDRA ++GLMG  P  +DP   ++ +   + +  L L G   IAFD  RD++ L  E 
Sbjct: 61  HATDRAVILGLMGFVPADLDPDAGEAALLDCQASQSLKLGGEVDIAFDEARDIVWLGHER 120

Query: 120 LPYHPNAMSLTAFGETGE-LFEQTYYSVGGGFIIEAAEAESGIAPAGDVVLPYDFSSAAE 178
           LP HPNA++  A+ + G+ L E+TY+S+GGGF+ + AE      P     +P+ F SAA+
Sbjct: 121 LPQHPNALTFAAYDKAGQVLAERTYFSIGGGFVRDEAEMGRNAPPDEGPAIPFPFESAAD 180

Query: 179 LLKLCNEHGLRVGELMMANERAWRSDAEIRQGLLHIWSVMRECVEQGLRHEGILPGGLSV 238
           LL+   + GL + E+M ANERA  S  E+  GL  I+  M  C+++G+R EG+LPGGL+V
Sbjct: 181 LLERAEQAGLSIAEVMAANERARMSQGEMDAGLDRIFGAMEACIDRGMRQEGVLPGGLTV 240

Query: 239 PRRAAKLHRSLQEIGKPNVITSTLSAMEWVNLYALAVNEENAAGGRMVTAPTNGAAGIIP 298
            RRA ++H+++Q       ++  L+AM++VNL+A+AVNEENAAGGR+VTAPTNGAAG+IP
Sbjct: 241 KRRARQIHQTIQG-RMERQMSDPLAAMDFVNLWAMAVNEENAAGGRVVTAPTNGAAGLIP 299

Query: 299 AVLHYYMKFNADASDDDVVAFFLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGL 358
           AVL ++++F    + + +  F L AAA+G L K+NASISGAEVGCQGEVG AC+MAAAGL
Sbjct: 300 AVLRFFVRFYK-GTPEQIRTFLLTAAAIGALYKRNASISGAEVGCQGEVGVACSMAAAGL 358

Query: 359 AEVLGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGD 418
           A  LG T  Q+ENAAEIG+EHNLGLTCDP+GGLVQ+PCIERNA+ A+KAI+A ++AL GD
Sbjct: 359 AAALGGTNAQIENAAEIGMEHNLGLTCDPIGGLVQIPCIERNAMGAIKAIDAARLALLGD 418

Query: 419 GKHFISLDRVIRTMRDTGADMHDKYKETSRGGLA----VNWVEC 458
           G+H +SLD+VI TM+ TG DM++ YKETS GGLA    VN VEC
Sbjct: 419 GQHSVSLDKVIATMKRTGEDMNEIYKETSMGGLAVGLSVNRVEC 462


Lambda     K      H
   0.320    0.135    0.404 

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: 539
Number of extensions: 19
Number of successful extensions: 5
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: 458
Length of database: 462
Length adjustment: 33
Effective length of query: 425
Effective length of database: 429
Effective search space:   182325
Effective search space used:   182325
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate CCNA_03206 CCNA_03206 (L-serine dehydratase)
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.8842.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8842.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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