GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araB in Shewanella sp. ANA-3

Align Ribulokinase (EC 2.7.1.16) (characterized)
to candidate 7024890 Shewana3_2064 ribulokinase (RefSeq)

Query= reanno::Cola:Echvi_0515
         (562 letters)



>FitnessBrowser__ANA3:7024890
          Length = 557

 Score =  607 bits (1564), Expect = e-178
 Identities = 298/550 (54%), Positives = 387/550 (70%), Gaps = 3/550 (0%)

Query: 5   FVIGLDYGSDSVRAVIVNTGNGEVKGSHVFWYPRWKAGKYCDPVNNQFRQHPLDHLEGLE 64
           + +GLDYGSDSVRA++V+T  G    ++V +YPRWK G +C+P  NQFRQHPLD++E L 
Sbjct: 8   YALGLDYGSDSVRALLVDTQTGAEVATNVVYYPRWKKGLFCEPAKNQFRQHPLDYIESLI 67

Query: 65  ETIREV-IKESGVPADQIKGICVDTTGSSPMAVDQQGKPLALSPEFAENPNAMMVLWKDH 123
           E ++ +  K     A ++ G+ VDTTGS+P+AVD+ G  LAL PEF  NPNAM +LWKDH
Sbjct: 68  EVVQGLWAKAPSGAAQRVCGLSVDTTGSTPIAVDESGVALALKPEFENNPNAMFLLWKDH 127

Query: 124 TAIKEADEINELARTWGGEDYTKYEGGIYSSEWFWAKILHVIREDDAVAQAAYSWMEHCD 183
           +AI EA +I   A     E+Y KYEGGIYSSEWFWAK L V+R D  V QAAYSW+EHCD
Sbjct: 128 SAIIEAKQITAAAND-SSENYLKYEGGIYSSEWFWAKALFVLRHDAEVRQAAYSWVEHCD 186

Query: 184 VITAELIGADNPLDVKRSRCAAGHKALWHESWDGLPPKEFLSKLDPRLADLRDRLYTETF 243
            ITA + G  +P   K  RCAAGHK +WHESW+G PP +F   +DP L  LRD+L  ET 
Sbjct: 187 WITALMTGTSHPKVFKAGRCAAGHKVMWHESWNGYPPNDFFVGIDPLLDGLRDKLPLETC 246

Query: 244 TSDLPAGNLSAEWAKKLGLSTDTVIAVGTFDAHAGAVGGEVTENTLVKVMGTSTCDIMVA 303
           TSD   G L+ EWA+ LGLST+ +++ G+FD HAGAVG  V    L KVMGTSTCDI VA
Sbjct: 247 TSDKVCGQLTPEWAQHLGLSTEVIVSFGSFDCHAGAVGANVKPGVLTKVMGTSTCDITVA 306

Query: 304 THEAIGDNLVKGICGQVDGSVIPGTVGLEAGQSGFGDVLAWFKHLVVKPTAALIRASNVL 363
           ++E IG+  +KGICGQVDGSV+PG +GLEAGQS FGD+ AWF+ L   P   L   S + 
Sbjct: 307 SYEDIGERCIKGICGQVDGSVLPGMIGLEAGQSAFGDLYAWFRDLTAWPMQQL-DTSVLF 365

Query: 364 DEEKKEALIHEIDSQLLIKLSEEAIQIPLSETAPVALDWVNGRRTPDANQALKGAVMGLN 423
           DE  K  LI +++S+ L  L   A +IP+ ET  VALDW+NGRRTPDA+Q++  A+ GL 
Sbjct: 366 DENIKAKLIQQLESETLTMLGNAAAKIPVGETGIVALDWINGRRTPDADQSVAMAITGLT 425

Query: 424 MGTDAARVFKALVESICFGSKKIVDRFREEGVAIDTVIGMGGVAKKSKLVMQTMADVLNM 483
           MG+ A +VFKALVE+  +G++ I++RF++EGV ID V+ +GG++KKS  +MQT ADV N 
Sbjct: 426 MGSQAPQVFKALVEASAYGARAIIERFKQEGVCIDHVVTIGGISKKSDFIMQTCADVWNC 485

Query: 484 PIKIATSDQAPALGAAMYASVAAGIHPTTEAAIAAMTNGFDKVYEPIPENVEVYKALYAK 543
            I +  S+Q+ ALGAA+YA+ AAG++P   +A AAM +   K Y+P PEN E Y+ALY  
Sbjct: 486 NIDVLESEQSCALGAAIYAATAAGVYPDVLSAQAAMASNVAKTYQPNPENAEKYQALYQG 545

Query: 544 YAEFGAFVEG 553
           Y   G +V+G
Sbjct: 546 YLALGHYVDG 555


Lambda     K      H
   0.316    0.133    0.398 

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: 881
Number of extensions: 41
Number of successful extensions: 4
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: 562
Length of database: 557
Length adjustment: 36
Effective length of query: 526
Effective length of database: 521
Effective search space:   274046
Effective search space used:   274046
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate 7024890 Shewana3_2064 (ribulokinase (RefSeq))
to HMM TIGR01234 (araB: ribulokinase (EC 2.7.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.23540.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23540.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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