GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pedobacter sp. GW460-11-11-14-LB5

Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate CA265_RS16605 CA265_RS16605 1-pyrroline-5-carboxylate dehydrogenase

Query= CharProtDB::CH_122352
         (572 letters)



>FitnessBrowser__Pedo557:CA265_RS16605
          Length = 544

 Score =  524 bits (1350), Expect = e-153
 Identities = 273/540 (50%), Positives = 358/540 (66%), Gaps = 7/540 (1%)

Query: 30  YKVPRIDNEPNKHYAAGSPDRKALQEALARTQRNAPLSVPLVIAGKEVKSSSSLTQSNPA 89
           + VP   NEP   YA G+ +R  L+EA+A   R+  L +P+ I G+EV + +      P 
Sbjct: 6   FNVPTPVNEPINSYAPGTKERSLLKEAIADA-RSKQLDIPMFIGGQEVHTKNKKKVVAPH 64

Query: 90  SHGPV-ATYSNATAKDVQAAIESALEARKSWASTPFADRASVFLKAADLISTKYRYDVMA 148
            H  V AT+S      V+ AI++AL A+  W +  +  RA++F+KAADLI+TKYRY + A
Sbjct: 65  DHQHVLATFSYGDKSHVKQAIDAALAAKADWEALAWEHRAAIFMKAADLIATKYRYQINA 124

Query: 149 LTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHHAPGVWNRVEYRPLEGFV 208
            TM GQ KNA+QAEID+A EL DF RF V Y +D+Y QQP     G+WNR E RPLEGF+
Sbjct: 125 ATMLGQSKNAYQAEIDAACELVDFLRFNVSYMQDIYGQQPPVSPNGMWNRTEQRPLEGFI 184

Query: 209 YAISPFNFTAIGGNLAGAPALMGNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQFVPG 268
           +A++PFNFTAI GNL    A+MGNVVVWKP+ + + +  ++ QI  EAGLP  VI  +  
Sbjct: 185 FALTPFNFTAIAGNLPACVAMMGNVVVWKPADTQVYAANVIMQIFREAGLPDGVINLIFA 244

Query: 269 EAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGKNFHL 328
           +  EV   V +H DFA +HFTGST VF+ ++  I T +   KY+SYPRIVGETGGK+F L
Sbjct: 245 DGPEVGDVVFNHADFAGIHFTGSTKVFQEIWKTIGTNI--HKYKSYPRIVGETGGKDFIL 302

Query: 329 IHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIADSFLEQVASEAKSLKVGPPSD 388
           +H SAD+  +A   VRGAFEYQGQKCSA SR Y+  S+     + +  +  S K+G   D
Sbjct: 303 VHPSADVAASATAIVRGAFEYQGQKCSAASRTYIPKSLWPEIKKLMIRDLASFKMGGTED 362

Query: 389 FTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGSYDSSKGWYIQPTVYRTTNPDHPL 448
           F+NF   VI E SF KLAK ID+AK D  +E++AGG+YD SKG++I+PT+    +P +  
Sbjct: 363 FSNFINAVIDERSFDKLAKYIDQAKKDKGVEVIAGGNYDKSKGYFIEPTILVVDDPKYTT 422

Query: 449 LTRELFGPILVVYAYPDATEADFARIAQKIDATGEYGLTGSVFAQDREALAVANDVLRNA 508
           +  ELFGP+L VY Y D    +F ++ + ID T  Y LTG++ +QDR A+  A+  LRN+
Sbjct: 423 MCEELFGPVLSVYVYED---QEFDQVLEIIDTTSPYALTGAILSQDRYAIEKASYALRNS 479

Query: 509 AGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSRFVSLRSIKEEFVPTYKVAYP 568
           AGNFYIN K TGAVVGQQPFGGAR SGTNDKAG+   L R+VS R+IKE F P     YP
Sbjct: 480 AGNFYINDKCTGAVVGQQPFGGARGSGTNDKAGAMINLLRWVSPRTIKETFNPPTDYRYP 539


Lambda     K      H
   0.316    0.130    0.379 

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: 876
Number of extensions: 30
Number of successful extensions: 5
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: 572
Length of database: 544
Length adjustment: 36
Effective length of query: 536
Effective length of database: 508
Effective search space:   272288
Effective search space used:   272288
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 CA265_RS16605 CA265_RS16605 (1-pyrroline-5-carboxylate dehydrogenase)
to HMM TIGR01236 (pruA: 1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

Software error:

../bin/blast/fastacmd -i /tmp/list.16438.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16438.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.