GapMind for Amino acid biosynthesis

 

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

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate 5210610 Shew_3038 asparagine synthase (glutamine-hydrolyzing) (RefSeq)

Query= CharProtDB::CH_007942
         (614 letters)



>FitnessBrowser__PV4:5210610
          Length = 590

 Score =  252 bits (644), Expect = 3e-71
 Identities = 176/554 (31%), Positives = 273/554 (49%), Gaps = 56/554 (10%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDI-EGG 59
           MCGI G + F      ++  +  M D L+ RGPD   ++       GH+RL ++D+ E G
Sbjct: 1   MCGIAGELSFTTSAKVDQ--VAAMLDKLAPRGPDGQGLYSLGPCCLGHRRLKIIDLSEHG 58

Query: 60  RQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVD 119
            QPM     G   T+++NG +YN   LR EL   G+ F   SD+EV+L +Y  W   CV+
Sbjct: 59  AQPMVDAELG--LTLVFNGCIYNYRALRAELSELGYHFFSHSDSEVILKAYAHWGRQCVE 116

Query: 120 HLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDR 179
             NG+FAFA+ +     LF ARDRLG+KP +Y K+G S +F S + A+L HP     +D 
Sbjct: 117 KFNGMFAFAIHERDTGRLFIARDRLGIKPLYYFKDGHSLVFASSLPALLRHPVADTEIDP 176

Query: 180 TGLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTFSKDG-LNIWRYWNVE--SEKHTDSFD 236
             L+            T +FK I ++  AH +    DG ++   YW++   S   T++ +
Sbjct: 177 QSLNHYLCFRAIVGDKT-LFKQIHKLEAAHWMLVRPDGQVDHQSYWHLSPGSSLETETEE 235

Query: 237 DTVANVRSLFQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYSIDY 296
                +     D+  R+L +DVPV   LSGGLDSS I     G   + G+  +HT+SI +
Sbjct: 236 TWSQQLEQKLFDSAKRRLEADVPVGVLLSGGLDSSLI----VGLLHELGQKEIHTFSIGF 291

Query: 297 EENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLPGMAD 356
           ++        A +  ++  + + + E + T H K V+S  +L+ HL + V+    P ++ 
Sbjct: 292 DD-------VADEQGNEFKYSDLIAEHYQTRHQKIVVSHSELISHLPDCVMAMSEPMVSH 344

Query: 357 VDSSLLWFCREIKKDFVVSLSGECADEIFGGYPWFHTADVESGFPWMRST-EERIKLLSD 415
                    + + +   V  SG+ ADE+FGGY W+         P + +T E+  +   D
Sbjct: 345 DVIGFYLLSKTVSQHVKVVQSGQGADEVFGGYHWYP--------PMVDATAEDEAQTYQD 396

Query: 416 ---SWQKKLNLKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLN---------MLWFM 463
              SWQ           +Y++ +AE PLLDG+   D  RR   +           ML   
Sbjct: 397 AYFSWQ---------YPEYQQLVAE-PLLDGDHAGDYVRRYFAHCPAETAIDKTLMLDTR 446

Query: 464 TNLLD----RKDRMSMGASLEVRVPFADHRLVEYVWNIPWEMKMHDNREKGILRKALEGI 519
             L+D    R D M+M   LE RVPF DH LVE    IP+++K+ +   K +L++    I
Sbjct: 447 VMLVDDPVKRVDNMTMAFGLEARVPFLDHELVELASRIPFDLKLKEG-GKYLLKQVARRI 505

Query: 520 LPDDILYRKKSPYP 533
           +P  ++ R K  +P
Sbjct: 506 IPHQVIDRPKGYFP 519


Lambda     K      H
   0.320    0.137    0.425 

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: 912
Number of extensions: 49
Number of successful extensions: 7
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: 614
Length of database: 590
Length adjustment: 37
Effective length of query: 577
Effective length of database: 553
Effective search space:   319081
Effective search space used:   319081
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: 53 (25.0 bits)

Align candidate 5210610 Shew_3038 (asparagine synthase (glutamine-hydrolyzing) (RefSeq))
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.20705.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20705.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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