GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Shewanella oneidensis MR-1

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate 201398 SO2248 L-serine dehydratase 1 (NCBI ptt file)

Query= BRENDA::P16095
         (454 letters)



>FitnessBrowser__MR1:201398
          Length = 458

 Score =  515 bits (1327), Expect = e-150
 Identities = 256/456 (56%), Positives = 333/456 (73%), Gaps = 6/456 (1%)

Query: 1   MISLFDMFKVGIGPSSSHTVGPMKAGKQFVDDLVEKGLLDSVTRVAVDVYGSLSLTGKGH 60
           MIS+FDMFK+GIGPSSSHTVGPMKAGK F+  L + G +  +  +  +++GSL  TGKGH
Sbjct: 1   MISVFDMFKIGIGPSSSHTVGPMKAGKIFMQHLADSGQIGQIDELRAELFGSLGQTGKGH 60

Query: 61  HTDIAIIMGLAGNEPATVDIDSIPGFIRDVEERERLLLAQGRHEVDFPRDNGMRFHNG-N 119
            T  A+I+GL G +P TVD DSI G +  V + E L ++ G+  V F R++G+ +H   +
Sbjct: 61  GTGKAVILGLMGEDPETVDTDSIDGILEHVSKSETLTISCGK-VVKFTREDGITYHRRKS 119

Query: 120 LPLHENGMQIHAYNGDEVVYSKTYYSIGGGFIVDEEHFGQDAANEVS----VPYPFKSAT 175
           LP H N M ++AY+  E ++ +TYYS+GGGFI+DE+   Q  A+  S     PY F S+ 
Sbjct: 120 LPAHANAMTLYAYSKGECIFERTYYSVGGGFILDEDEINQRNASPASQIESAPYDFNSSA 179

Query: 176 ELLAYCNETGYSLSGLAMQNELALHSKKEIDEYFAHVWQTMQACIDRGMNTEGVLPGPLR 235
           +LL  C E G S+S L M NEL+L S++E+     ++WQTM+ CI+RG   EG+LPG L+
Sbjct: 180 QLLELCTEHGLSISSLMMANELSLASEEEVKAKLWNIWQTMKTCIERGYQKEGILPGGLK 239

Query: 236 VPRRASALRRMLVSSDKLSNDPMNVIDWVNMFALAVNEENAAGGRVVTAPTNGACGIVPA 295
           + RRA AL R L +  + + DP+  +DWV++FAL+VNE+NAAG RVVTAPTNGA GI+PA
Sbjct: 240 LRRRAPALYRRLKAEGRNNVDPLTAMDWVDLFALSVNEQNAAGDRVVTAPTNGAAGIIPA 299

Query: 296 VLAYYDHFIESVSPDIYTRYFMAAGAIGALYKMNASISGAEVGCQGEVGVACSMAAAGLA 355
           VL YYD F++ V  D+  RY + A AIG LYK NASISGAEVGCQGEVGVACSMAA  L 
Sbjct: 300 VLCYYDTFVQEVDIDVCARYLLTAAAIGILYKKNASISGAEVGCQGEVGVACSMAAGALT 359

Query: 356 ELLGGSPEQVCVAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINAARMALRRTS 415
           E++GG+ E V  AAEIGMEHNLGLTCDPV G VQVPCIERNA+ ++KAINA+RMALR   
Sbjct: 360 EIMGGTVEHVENAAEIGMEHNLGLTCDPVGGLVQVPCIERNAMGAIKAINASRMALRGDG 419

Query: 416 APRVSLDKVIETMYETGKDMNAKYRETSRGGLAIKV 451
             +VSLDKVI+TM +TGKDM +KY+ET++GGLA+ +
Sbjct: 420 NHKVSLDKVIKTMMDTGKDMRSKYKETAKGGLAVNI 455


Lambda     K      H
   0.318    0.135    0.396 

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: 629
Number of extensions: 26
Number of successful extensions: 3
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: 454
Length of database: 458
Length adjustment: 33
Effective length of query: 421
Effective length of database: 425
Effective search space:   178925
Effective search space used:   178925
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 201398 SO2248 (L-serine dehydratase 1 (NCBI ptt file))
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.20519.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20519.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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