GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Shewanella loihica PV-4

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate 5209147 Shew_1625 L-serine dehydratase 1 (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5557
         (458 letters)



>FitnessBrowser__PV4:5209147
          Length = 458

 Score =  515 bits (1326), Expect = e-150
 Identities = 275/463 (59%), Positives = 338/463 (73%), Gaps = 13/463 (2%)

Query: 3   LSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKGHG 62
           +SVFD+FKIGIGPSSSHTVGPM+A   F + L +   L  T  ++ EL+GSLG TGKGHG
Sbjct: 2   ISVFDMFKIGIGPSSSHTVGPMKAGNIFIQDLEKHGHLAETDELRSELFGSLGQTGKGHG 61

Query: 63  SDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMIR-KPLA 121
           + KAV+LGL GE P+TVDT+ +DA L  +  +  L +     + F+ +  +   R K L 
Sbjct: 62  TGKAVILGLMGEAPETVDTDKIDATLAQVHDTQSLTMPNNKVVRFSREDGITYHRRKSLP 121

Query: 122 FHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLT------FPFK 175
            H N M   A+ A G  +  R YYSVGGGF++DE     + + +DA+P +      + F 
Sbjct: 122 AHANAMTLYAY-AKGNCIYQRTYYSVGGGFILDED----EILAQDASPASPIEAAPYDFN 176

Query: 176 SAKDLLGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPG 235
           SA +LL  C   GLSIS +M+ NE +   E E +  L  IWQ M+ CV  G + EGILPG
Sbjct: 177 SAAELLDMCVENGLSISALMMENELSIASEKEVKERLWTIWQTMKSCVERGYQKEGILPG 236

Query: 236 GLKVKRRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAG 295
           GLK++RRA AL+R+L K     + DPL+ +DWV+L+ALAVNE+NA G RVVTAPTNGAAG
Sbjct: 237 GLKLRRRAPALYRRL-KAESKTVVDPLTAMDWVDLFALAVNEQNAAGDRVVTAPTNGAAG 295

Query: 296 IIPAVLHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAA 355
           IIPAVL YY  F+     D   ++LLTAAAIGILYK+NASISGAEVGCQGEVGVACSMAA
Sbjct: 296 IIPAVLCYYDTFVQEVDLDICCQYLLTAAAIGILYKKNASISGAEVGCQGEVGVACSMAA 355

Query: 356 GALCEVLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAM 415
            AL E++GG+V+ VENAAEIGMEHNLGLTCDP+GGLVQVPCIERNAMG+VKAINA R+AM
Sbjct: 356 AALTEIMGGTVEHVENAAEIGMEHNLGLTCDPVGGLVQVPCIERNAMGAVKAINASRLAM 415

Query: 416 RGDGHHFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458
           RGDG+H VSLDKVI+TM  TG DM+SKYKETA+GGLAVNI+EC
Sbjct: 416 RGDGNHKVSLDKVIKTMMDTGKDMRSKYKETAKGGLAVNIVEC 458


Lambda     K      H
   0.320    0.136    0.401 

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: 654
Number of extensions: 18
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: 458
Length of database: 458
Length adjustment: 33
Effective length of query: 425
Effective length of database: 425
Effective search space:   180625
Effective search space used:   180625
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 5209147 Shew_1625 (L-serine dehydratase 1 (RefSeq))
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.20391.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20391.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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