GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Shewanella amazonensis SB2B

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 6937472 Sama_1628 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>FitnessBrowser__SB2B:6937472
          Length = 405

 Score =  534 bits (1375), Expect = e-156
 Identities = 261/402 (64%), Positives = 314/402 (78%)

Query: 5   ITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKAL 64
           I RS FDE M+P YAP+  IPV+G GSRLWDQQG+E+IDFAGGIAVN LGH HP LV AL
Sbjct: 3   INRSLFDEVMVPNYAPSPIIPVKGLGSRLWDQQGREFIDFAGGIAVNCLGHCHPALVSAL 62

Query: 65  TEQAGKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRF 124
           TEQA K WH  N  TNEP L LAK L+D TFA++V+F NSGAEANEAALKL R+ A ++F
Sbjct: 63  TEQAQKLWHLSNTMTNEPALMLAKHLVDNTFAEKVYFANSGAEANEAALKLVRRVALNKF 122

Query: 125 GSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNT 184
           G++KS I+AFK  FHGRTLFTVS GGQPAYS  F P P  I HA YN+LDS KALI D T
Sbjct: 123 GADKSQIIAFKQGFHGRTLFTVSVGGQPAYSDGFGPKPADIDHAEYNNLDSLKALISDRT 182

Query: 185 CAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVT 244
           CAV++EP+QGEGG++    +F++G+RELCD HNALL+FDEVQTGVGRTGELYAYM  GVT
Sbjct: 183 CAVVLEPLQGEGGIINPTPEFIKGVRELCDQHNALLVFDEVQTGVGRTGELYAYMGLGVT 242

Query: 245 PDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREV 304
           PD+L+TAKALGGGFPIGA+L +   A  + VGTHG+TYGGNPLACAV    F T+NT EV
Sbjct: 243 PDVLTTAKALGGGFPIGAMLTTTELAKHLVVGTHGSTYGGNPLACAVGLAAFTTVNTPEV 302

Query: 305 LNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLM 364
           LNGVK+R Q F + LNAIN +Y +F E+RG GLL+G  L  +YAGKA+     AAEEG++
Sbjct: 303 LNGVKEREQLFRDGLNAINDKYQVFTEVRGKGLLLGAALNADYAGKARDFMLAAAEEGVL 362

Query: 365 ILIAGANVVRFAPALIISEDEVNSGLDRFELACKRFLAGVSS 406
           +L+AG NVVRFAP+LII E +V  GL RF+ A  + +A +++
Sbjct: 363 LLMAGQNVVRFAPSLIIPEADVREGLARFDAAIAKLVARLNA 404


Lambda     K      H
   0.321    0.137    0.412 

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: 522
Number of extensions: 17
Number of successful extensions: 1
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: 406
Length of database: 405
Length adjustment: 31
Effective length of query: 375
Effective length of database: 374
Effective search space:   140250
Effective search space used:   140250
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: 50 (23.9 bits)

Align candidate 6937472 Sama_1628 (bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq))
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

Software error:

../bin/blast/fastacmd -i /tmp/list.19033.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19033.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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