GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Desulfovibrio vulgaris Hildenborough

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate 207626 DVU2147 L-serine dehydratase, putative

Query= reanno::Miya:8499231
         (459 letters)



>MicrobesOnline__882:207626
          Length = 502

 Score =  648 bits (1671), Expect = 0.0
 Identities = 350/502 (69%), Positives = 381/502 (75%), Gaps = 43/502 (8%)

Query: 1   MQPLV--ATIETSLFDMFEAGPGPSSSHTIGPMKAGHDFRTLCAALPPEVLACAADIRVR 58
           MQPLV  + I  SLFD+FEAGPGPSSSHTIGPMKAG+DF   CA LP ++L  AA +RVR
Sbjct: 1   MQPLVPCSAIAISLFDLFEAGPGPSSSHTIGPMKAGYDFAQRCATLPDDILCRAAGVRVR 60

Query: 59  LFGSLSATGVGHGTTGAVLAGLLGHRPATCPPGLL-------ESLPA----LPEGERTLR 107
           LFGSLSATG GHGT  AVLAGL G  PA+CPP  L       E  PA    L +G     
Sbjct: 61  LFGSLSATGYGHGTDMAVLAGLAGQLPASCPPEYLVRPEGAGEERPATDTTLADGRYASL 120

Query: 108 LG-------PAA-----------------------LVLAEGTVRRDAVQHAYPFSNTLVM 137
           LG       P A                       L L    V  DAVQH +PFSNTLV+
Sbjct: 121 LGCEGVVPVPVAGQGQGHSASGAVVRYMMLRDGLRLPLTSACVVHDAVQHEHPFSNTLVL 180

Query: 138 ELLDAHGAVLCEREYYSVGGGFIQWKGWQPEERGRPAHPYRSMAQLRARLVETGLTIHEL 197
           ELL   GA L    YYSVGGGFIQW+GWQPEERG P HPY +M QLR  + +TGL +HE+
Sbjct: 181 ELLGDTGASLFSYTYYSVGGGFIQWEGWQPEERGAPVHPYCTMRQLRECMDDTGLALHEI 240

Query: 198 ILENEMAVTGMGRAAILDRLAAIIELMEASVRRGIEDGGPLPGTLGVHRKARVLLMRAQR 257
           ILENEMAVTG  RA+I+ RL  II LMEASV RG+   G LPGTLGV RKA  L+ RA +
Sbjct: 241 ILENEMAVTGASRASIVARLDTIIGLMEASVERGLATTGRLPGTLGVFRKASTLMARAGK 300

Query: 258 LPNEVDVFLGRLNAYAFAAAEENAAGGVIVTAPTCGAAGVMPALLYAMRHDLAIGDRAVR 317
           LP+ VD FL RLNAYAFA +EENA+GGVIVTAPTCGAAGVMPA+LYAMR+D +IGDRAVR
Sbjct: 301 LPHAVDAFLCRLNAYAFAVSEENASGGVIVTAPTCGAAGVMPAVLYAMRNDFSIGDRAVR 360

Query: 318 EGVLASAAVGFLAKHNAGIAGAEVGCQGEVGVASAMAAAMLAHARGNPVHVVENAAEIAL 377
           EGVLASAAVGFLAK NAGIAGAEVGCQGEVGVASAMAAAMLAHARGN V VVENAAEIAL
Sbjct: 361 EGVLASAAVGFLAKQNAGIAGAEVGCQGEVGVASAMAAAMLAHARGNAVRVVENAAEIAL 420

Query: 378 EHHLGLTCDPVGGYVQIPCIERNAVGAVKAYNACLLATCEDPRHHRVTLDSVIAAMAEIG 437
           EHHLGLTCDPVGGYVQIPCIERNAVGAVKAYNACL+ATCEDP+HHRVTLD+VI AMAEIG
Sbjct: 421 EHHLGLTCDPVGGYVQIPCIERNAVGAVKAYNACLVATCEDPKHHRVTLDNVIRAMAEIG 480

Query: 438 RDMNAKFKETSSGGLAVSVVEC 459
            DMNAKFKETS+GGLAVSVVEC
Sbjct: 481 HDMNAKFKETSAGGLAVSVVEC 502


Lambda     K      H
   0.321    0.136    0.406 

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: 706
Number of extensions: 25
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 459
Length of database: 502
Length adjustment: 34
Effective length of query: 425
Effective length of database: 468
Effective search space:   198900
Effective search space used:   198900
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 207626 DVU2147 (L-serine dehydratase, putative)
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.20232.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20232.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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