GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Shewanella amazonensis SB2B

Align N-acetylgalactosamine-6-phosphate deacetylase; GalNAc-6-P deacetylase; N-acetylglucosamine-6-phosphate deacetylase; GlcNAc-6-P deacetylase; EC 3.5.1.-; EC 3.5.1.25 (characterized)
to candidate 6937024 Sama_1198 N-acetylglucosamine-6-phosphate deacetylase (RefSeq)

Query= SwissProt::A0KYQ5
         (394 letters)



>FitnessBrowser__SB2B:6937024
          Length = 411

 Score =  360 bits (924), Expect = e-104
 Identities = 199/386 (51%), Positives = 245/386 (63%), Gaps = 5/386 (1%)

Query: 4   NTDFMLIA--DGAKVLTQGNLTEHCAIEVSDGIICGLKSTISAEWTADKPHYRLTSGTLV 61
           N +F+L+   D ++    GN       +V   I  G   TIS     D P YRL  G L 
Sbjct: 19  NPEFVLVGADDASEFGVTGNAIAALVPDVWLKISQGHIETISRRPDVDLPQYRLP-GILA 77

Query: 62  AGFIDTQVNGGGGLMFNHVPTLETLRLMMQAHRQFGTTAMLPTVITDDIEVMQAAADAVA 121
              +DTQVNGGGG++ NH PT   +  + Q H Q+GT A+LPTVI+D++ VM+ A D   
Sbjct: 78  PALVDTQVNGGGGVLINHQPTAAGINTLTQTHGQYGTGALLPTVISDNLAVMEQALDGAI 137

Query: 122 EAIDCQVPGIIGIHFEGPHLSVAKRGCHPPAHLRGITEREWLLYLRQ--DLGVRLITLAP 179
            A       ++GIHFEGPHLS+AK+GCH PA +R I E E  LY      LG  ++TLAP
Sbjct: 138 AARQGGDAAVVGIHFEGPHLSLAKKGCHSPALIRPIGEAEMTLYADAVAALGCCMVTLAP 197

Query: 180 ESVTPEQIKRLVASGAIISLGHSNADGETVLKAIEAGASGFTHLYNGMSALTSREPGMVG 239
           E+V P  I RLVA G  +SLGHSNAD  TV  ++ AGASGFTHL+NGMSAL  REPGMVG
Sbjct: 198 ETVEPADIARLVALGVRVSLGHSNADVATVEASLAAGASGFTHLFNGMSALQGREPGMVG 257

Query: 240 AAFASENTYCGIILDGQHVHPISALAAWRAKGTEHLMLVTDAMSPLGSDQTEFQFFDGKV 299
           AA A    YCGIILDG+HVH  SA  AWR KGT  LMLVTDAMSP G+ +  F+FF GKV
Sbjct: 258 AALACPEAYCGIILDGEHVHATSATLAWRLKGTRRLMLVTDAMSPTGTREESFEFFGGKV 317

Query: 300 VREGMTLRDQHGSLAGSVLDMASAVRYAATELNLGLSNAVQMATRTPAEFIQRPQLGDIA 359
            R+GM LRD+ GSLAGSVL M +AVR A   L +  + A+ MAT TPA F+    +G +A
Sbjct: 318 HRDGMVLRDEQGSLAGSVLTMTAAVRQACAMLGVSAAEALWMATATPAAFLGLKDIGRLA 377

Query: 360 EGKQADWVWLDDDQRVLAVWIAGELL 385
            G +AD + LDD    L  W AG+L+
Sbjct: 378 PGNRADLLLLDDALYQLGRWQAGQLV 403


Lambda     K      H
   0.320    0.134    0.400 

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: 497
Number of extensions: 12
Number of successful extensions: 2
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: 394
Length of database: 411
Length adjustment: 31
Effective length of query: 363
Effective length of database: 380
Effective search space:   137940
Effective search space used:   137940
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 6937024 Sama_1198 (N-acetylglucosamine-6-phosphate deacetylase (RefSeq))
to HMM TIGR00221 (nagA: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.3211.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3211.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.