GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoA in Acidovorax sp. GW101-3H11

Align Putative thymidine phosphorylase; EC 2.4.2.4; TdRPase (uncharacterized)
to candidate Ac3H11_2202 Thymidine phosphorylase (EC 2.4.2.4)

Query= curated2:Q21W90
         (522 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2202
          Length = 535

 Score =  820 bits (2117), Expect = 0.0
 Identities = 409/511 (80%), Positives = 461/511 (90%)

Query: 12  SKLVLRRVAIDTYRENVAYLHRDCAVYRAEGFQALSKVEVRANGRHILATLNVVDDPNIV 71
           S+L LRRVAIDT+RENVAYLHRDCAVYRAEGFQALSK+EVRANGR ILAT+NVVDDP IV
Sbjct: 25  SQLALRRVAIDTWRENVAYLHRDCAVYRAEGFQALSKIEVRANGRRILATVNVVDDPAIV 84

Query: 72  ACNELGLSEDAFAQMAVIDGQPASVSQAEPPQSIGALRRKLAGERLGREDFLGIVRDIAE 131
            C ELGLSEDAFAQ+ V +G   SV+QAEPP+S+GAL RK+A ERL REDF  IVRDIA+
Sbjct: 85  GCQELGLSEDAFAQLGVDNGHTVSVAQAEPPESMGALFRKIASERLTREDFGAIVRDIAD 144

Query: 132 LHYSKIELSAFVVATNRDELDREEVYFLTEAMVASGRTLNWHEPLVVDKHCIGGIPGNRS 191
             YSKIEL+AFVVA +R ELDREEV+FLT+AMVASGR L+WHEPLVVDKHCIGGIPGNR+
Sbjct: 145 HRYSKIELTAFVVACHRSELDREEVFFLTDAMVASGRRLDWHEPLVVDKHCIGGIPGNRT 204

Query: 192 SMLVVPIVAAHGLLCPKTSSRAITSPAGTADTMEVLAKVELPVDQLADIVRTHRGCLAWG 251
           +MLVVPIVAAHG+LCPKTSSRAITSPAGTADTMEVLAKVELP++QLADIVR +RGCLAWG
Sbjct: 205 TMLVVPIVAAHGMLCPKTSSRAITSPAGTADTMEVLAKVELPLEQLADIVRDYRGCLAWG 264

Query: 252 GAAHLSPADDVLISVERPLAIDSPGQMVASILSKKIAAGSTHLVLDIPIGPSAKVRSMPE 311
           G AHLSPADDVLISVERPL+IDS GQMVASILSKK+AAG+THLVLDIPIGP+AKVRSMP+
Sbjct: 265 GTAHLSPADDVLISVERPLSIDSAGQMVASILSKKVAAGATHLVLDIPIGPTAKVRSMPD 324

Query: 312 AQRLRRLFEYVAGRMHLSLDVVVTDGRQPIGNGIGPVLEARDVMRVLENDPRAPNDLRQK 371
           AQRLRRLFEYVA RM LSLDVV+TDGRQP+G G+GPVLEARDVMRVL+NDPRAP+DLRQK
Sbjct: 325 AQRLRRLFEYVARRMGLSLDVVITDGRQPVGQGVGPVLEARDVMRVLQNDPRAPDDLRQK 384

Query: 372 SLRLAGRLIEFDPDVRGGDGFAIARDILDSGRALAKMNAIIAAQGAKPFDHNHPQLGALT 431
           +LRLAGRLIE DPDVRGGDG+AIARDILDSGRALA+MNAIIAAQG+  FDHNHP LGALT
Sbjct: 385 ALRLAGRLIECDPDVRGGDGYAIARDILDSGRALARMNAIIAAQGSTGFDHNHPALGALT 444

Query: 432 FDICASESGVVTGIDNLQVARIARLAGAPKVIGAGIDLFHKLGEAVTSGEVLYRVHAGFQ 491
            D+ A  SGVV+ IDN Q+A +ARLAGAPKV GAG+DL HKLG+ V +G++LYRVHA + 
Sbjct: 445 LDVVAPASGVVSAIDNYQIACVARLAGAPKVPGAGVDLMHKLGDTVAAGDLLYRVHASYP 504

Query: 492 SDLDFARQACAKSTGYTLGRAEDVPHVFTEF 522
           +DL+FAR AC + +GY LG A++VP VF EF
Sbjct: 505 ADLEFARHACERDSGYRLGTADEVPQVFVEF 535


Lambda     K      H
   0.320    0.137    0.396 

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: 971
Number of extensions: 30
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: 522
Length of database: 535
Length adjustment: 35
Effective length of query: 487
Effective length of database: 500
Effective search space:   243500
Effective search space used:   243500
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 Ac3H11_2202 (Thymidine phosphorylase (EC 2.4.2.4))
to HMM TIGR02645 (putative thymidine phosphorylase (EC 2.4.2.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.18847.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18847.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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