GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcB in Shewanella amazonensis SB2B

Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate 6938261 Sama_2381 malate synthase (RefSeq)

Query= reanno::MR1:200654
         (549 letters)



>FitnessBrowser__SB2B:6938261
          Length = 543

 Score =  911 bits (2354), Expect = 0.0
 Identities = 449/548 (81%), Positives = 481/548 (87%), Gaps = 9/548 (1%)

Query: 1   MTEHTLSEQQVNLTLNKATANGTLALVGNTIPGQEVIFTEGAMALLESLCREFGAEVPTL 60
           MTE  + + Q        T  G L L G+ I GQE +FTEGAM+LLESLC  F  +V  L
Sbjct: 1   MTEQMMEQPQ--------TLTG-LKLAGHHIQGQEEVFTEGAMSLLESLCARFAGDVDAL 51

Query: 61  LAKRKDRQARIDKGALPDFLPETRAIRDGAWKIRGIPNDLLDRRVEITGPVERKMVINAL 120
           LAKRK+RQ RIDKG LPDFLPETRAIRDG W IRGIP DL DRRVEITGPV+RKM+INAL
Sbjct: 52  LAKRKERQVRIDKGELPDFLPETRAIRDGKWTIRGIPTDLQDRRVEITGPVDRKMIINAL 111

Query: 121 NANAKVFMADFEDSLAPSWQKVVEGQINLRDAVRGEIEYTAPETGKHYKLGPNPAVLICR 180
           NA+ KVFMADFEDSLAPSW+KV++GQINLRDAVRG IEY AP+TGK Y+L  NPAVLI R
Sbjct: 112 NADVKVFMADFEDSLAPSWEKVIQGQINLRDAVRGTIEYKAPDTGKEYRLNDNPAVLIAR 171

Query: 181 VRGLHLKEKHVEFNQQSIPGGLFDFAMYFYHNYRQLLAKGSGPYFYIPKLESHIEARWWA 240
           VRGLHLKEKHVEFN QSIPG LFDF  YFYHNYRQLL+KGSGPYFYIPKLESH+EARWWA
Sbjct: 172 VRGLHLKEKHVEFNGQSIPGALFDFCFYFYHNYRQLLSKGSGPYFYIPKLESHLEARWWA 231

Query: 241 KVFAFVEERFCLQAGTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKT 300
           KVFAF EERFCL+ GTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKT
Sbjct: 232 KVFAFTEERFCLEPGTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKT 291

Query: 301 LKRHGDRVLPDRQAVTMDTPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKDPAQNEAVL 360
           LK H DRVLPDRQ VTMD PFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKD   N  VL
Sbjct: 292 LKHHSDRVLPDRQQVTMDKPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKDAEANRLVL 351

Query: 361 QRVRKDKELEARNGHDGTWVAHPGLADTAMGIFNEYIGQDHQNQLHITRDVDAPILAAEL 420
           +RV KDKELEARNGHDGTWVAHPGLA TAM +FN++IG DH NQLHITRDVDAPILA+EL
Sbjct: 352 ERVCKDKELEARNGHDGTWVAHPGLAQTAMAVFNQFIGDDHCNQLHITRDVDAPILASEL 411

Query: 421 LKTCDGERTEQGMRLNIRIALQYLEAWISGNGCVPIYGLMEDAATAEISRASIWQWIQHG 480
           L  C+GERTE GMRLNIRIALQY+EAWISGNGCVPIYGLMEDAATAEISRASIWQWI H 
Sbjct: 412 LAPCEGERTEHGMRLNIRIALQYIEAWISGNGCVPIYGLMEDAATAEISRASIWQWIHHQ 471

Query: 481 KSLSNGKLVTKQLFKDMLVEELANVKKEVGSDRFTHGKFTQAAVLLEDITTSDELVDFLT 540
           K LSNGKLVTK L K+MLVEELANVK+EVGS+RFTHG+FTQAAVLLE+ITT+DELVDFLT
Sbjct: 472 KHLSNGKLVTKALLKEMLVEELANVKEEVGSERFTHGRFTQAAVLLEEITTADELVDFLT 531

Query: 541 LPGYEMLT 548
           LPGYE+LT
Sbjct: 532 LPGYELLT 539


Lambda     K      H
   0.321    0.137    0.411 

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: 1004
Number of extensions: 22
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: 549
Length of database: 543
Length adjustment: 35
Effective length of query: 514
Effective length of database: 508
Effective search space:   261112
Effective search space used:   261112
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: 52 (24.6 bits)

Align candidate 6938261 Sama_2381 (malate synthase (RefSeq))
to HMM TIGR01344 (aceB: malate synthase A (EC 2.3.3.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.14283.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14283.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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