GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Pseudomonas simiae WCS417

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate GFF4367 PS417_22360 glycine dehydrogenase

Query= reanno::WCS417:GFF4367
         (946 letters)



>FitnessBrowser__WCS417:GFF4367
          Length = 946

 Score = 1890 bits (4896), Expect = 0.0
 Identities = 946/946 (100%), Positives = 946/946 (100%)

Query: 1   MTVQLTTANEFIARHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLS 60
           MTVQLTTANEFIARHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLS
Sbjct: 1   MTVQLTTANEFIARHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLS 60

Query: 61  EAEALAKIKAIAGKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGR 120
           EAEALAKIKAIAGKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGR
Sbjct: 61  EAEALAKIKAIAGKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGR 120

Query: 121 LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASIHSHPQT 180
           LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASIHSHPQT
Sbjct: 121 LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASIHSHPQT 180

Query: 181 LDVLRTRAEPLGIDVVVGDERELTDVSPFFGALLQYPASNGDVFDYRELTERFHAAHGLV 240
           LDVLRTRAEPLGIDVVVGDERELTDVSPFFGALLQYPASNGDVFDYRELTERFHAAHGLV
Sbjct: 181 LDVLRTRAEPLGIDVVVGDERELTDVSPFFGALLQYPASNGDVFDYRELTERFHAAHGLV 240

Query: 241 AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG 300
           AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG
Sbjct: 241 AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG 300

Query: 301 VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARR 360
           VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARR
Sbjct: 301 VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARR 360

Query: 361 VHQLTAILAKGLTALGQNVEQAHFFDTLTLNTGANTAAVHDKARAQRINLRVVDAERVGV 420
           VHQLTAILAKGLTALGQNVEQAHFFDTLTLNTGANTAAVHDKARAQRINLRVVDAERVGV
Sbjct: 361 VHQLTAILAKGLTALGQNVEQAHFFDTLTLNTGANTAAVHDKARAQRINLRVVDAERVGV 420

Query: 421 SVDETTTQADIETLWAIFADGKALPDFAAQVESTLPAALLRQSPVLSHPVFNRYHSETEL 480
           SVDETTTQADIETLWAIFADGKALPDFAAQVESTLPAALLRQSPVLSHPVFNRYHSETEL
Sbjct: 421 SVDETTTQADIETLWAIFADGKALPDFAAQVESTLPAALLRQSPVLSHPVFNRYHSETEL 480

Query: 481 MRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYLEL 540
           MRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYLEL
Sbjct: 481 MRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYLEL 540

Query: 541 TSDLEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAHGTN 600
           TSDLEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAHGTN
Sbjct: 541 TSDLEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAHGTN 600

Query: 601 PATANMAGMRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIREIC 660
           PATANMAGMRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIREIC
Sbjct: 601 PATANMAGMRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIREIC 660

Query: 661 GIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKS 720
           GIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKS
Sbjct: 661 GIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKS 720

Query: 721 HLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYISMMGGAGLKRASQLAILNANYIS 780
           HLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYISMMGGAGLKRASQLAILNANYIS
Sbjct: 721 HLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYISMMGGAGLKRASQLAILNANYIS 780

Query: 781 RRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAG 840
           RRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAG
Sbjct: 781 RRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAG 840

Query: 841 TLMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPHTAAELVSEWTH 900
           TLMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPHTAAELVSEWTH
Sbjct: 841 TLMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPHTAAELVSEWTH 900

Query: 901 PYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 946
           PYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA
Sbjct: 901 PYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 946


Lambda     K      H
   0.319    0.135    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: 2509
Number of extensions: 77
Number of successful extensions: 3
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: 946
Length of database: 946
Length adjustment: 44
Effective length of query: 902
Effective length of database: 902
Effective search space:   813604
Effective search space used:   813604
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: 57 (26.6 bits)

Align candidate GFF4367 PS417_22360 (glycine dehydrogenase)
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.8729.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8729.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.