GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Synechococcus elongatus PCC 7942

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate Synpcc7942_2079 Synpcc7942_2079 acetate kinase

Query= curated2:Q8YU00
         (405 letters)



>FitnessBrowser__SynE:Synpcc7942_2079
          Length = 393

 Score =  337 bits (864), Expect = 4e-97
 Identities = 189/405 (46%), Positives = 256/405 (63%), Gaps = 19/405 (4%)

Query: 1   MKVLILNAGSSSQKSCLYEIPDDALLSEAPQPLWEGKVNWTQDRSVAEIEVKTARGETLH 60
           +++L  NAGSSS K   +EI   A   E   P+W+ +++W  DR+       T  G+ + 
Sbjct: 1   LQLLTFNAGSSSYKLSGFEITTAA---EQTDPVWQVQIDWKTDRAAT----LTQPGQPV- 52

Query: 61  ESIYGDSRQAHVTYMLYTLSRGATKVIGQLSEIDVVGHRVVHGGQNYRHSVIITEEVKQA 120
           + +    R+A +   L TL           S I  V HRVVHGGQ    +V+ T E+K  
Sbjct: 53  QMLDSSDRRAWLEIALETLP--------DRSAIAAVVHRVVHGGQQQAPAVV-TPELKAT 103

Query: 121 IAKLSNLAPAHNPAALEGIEAIEKSLG-DVPQVAVFDTGFHATLPDAAAIYPGPFEWVEQ 179
           IA  +NLAP HNP  L GIE +E+  G  +PQ+AVFDT FH  +P AAAIY GP+ W EQ
Sbjct: 104 IAAAANLAPLHNPLNLAGIEQMEQLFGLAMPQIAVFDTAFHQQMPVAAAIYGGPYHWWEQ 163

Query: 180 GIRRYGFHGISHQYCSARAAQILGRDLASLRIITCHLGNGCSLAAIKNGRSIDTTMGFTP 239
           G RRYGFHGISHQY + R AQ+  R L++L+++T HLGNGCSLAAI+NG S+DT+MGF+P
Sbjct: 164 GYRRYGFHGISHQYLAERCAQLSDRSLSNLQLVTAHLGNGCSLAAIRNGHSVDTSMGFSP 223

Query: 240 LDGLMMGSRSGAIDPGIIVHLMRQSDYSAERLDYVLNKASGLRGISGVSSDLPQVIEAIT 299
           L+GL+MGSRSG +DPG+++HL++Q D S  +L  VLN+ SGL G+SG S+D+  +  A  
Sbjct: 224 LEGLVMGSRSGTVDPGLLLHLLQQPDCSPSQLSTVLNQQSGLLGLSGRSNDVRALAIAAD 283

Query: 300 QGNYRAQLAWDMYVHRLRSGIGSMLASLGGLDVLVFTAGVGEKSAGIRQAACEAFGFLGL 359
            G+ R+QLA   + H LR  +G+MLASL  LD LVF  G+GE    +  A CE F  + +
Sbjct: 284 AGDQRSQLALAAFTHSLRRHLGAMLASLTRLDALVFAGGIGENYRSLWPAVCEHFAGMPI 343

Query: 360 KLDPEKNQNKPVDIDIATADSTVRVLVIHTQEDWAIAQQCWHLLK 404
           +LDPE       D  I+T DS + V VIH++EDW + Q    LL+
Sbjct: 344 RLDPEA-MAVAGDRRISTPDSAITVWVIHSREDWQMVQLALPLLR 387


Lambda     K      H
   0.319    0.135    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: 428
Number of extensions: 15
Number of successful extensions: 6
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: 405
Length of database: 393
Length adjustment: 31
Effective length of query: 374
Effective length of database: 362
Effective search space:   135388
Effective search space used:   135388
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 Synpcc7942_2079 Synpcc7942_2079 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.25858.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25858.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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