GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaZ2 in Paraburkholderia bryophila 376MFSha3.1

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate H281DRAFT_00370 H281DRAFT_00370 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (EC 1.2.1.77)

Query= BRENDA::P77455
         (681 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00370 H281DRAFT_00370
           3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (EC
           1.2.1.77)
          Length = 531

 Score =  415 bits (1067), Expect = e-120
 Identities = 229/524 (43%), Positives = 320/524 (61%), Gaps = 14/524 (2%)

Query: 1   MQQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMT 60
           ++ L + ++G W +G G    +   ++GEAL  V+SEGLD++ A +FA ++  P+LRA+T
Sbjct: 2   IELLKNHVAGEWVAGTGDGHTLTDPVTGEALVRVSSEGLDLSHAFRFARDEAGPSLRALT 61

Query: 61  FIERAAMLKAVAKHLLSEKERFYALS-AQTGATRADSWVDIEGGIGTLFTYASLGSRELP 119
           + ERAA L  V K L S+++ +YA++ A +G TR DS VDI+GGI TL  YA LG+  L 
Sbjct: 62  YAERAARLADVVKLLQSKRDDYYAIALANSGTTRNDSAVDIDGGIFTLSYYARLGA-SLG 120

Query: 120 DDTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAI 179
           +     +     LSK+  F+ +H+LT   GVA+ INAFNFP WG+ EK AP  L G+P I
Sbjct: 121 NVHALRDGNASALSKDQSFSVQHVLTPTRGVALFINAFNFPSWGLWEKAAPALLSGLPVI 180

Query: 180 IKPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQM 239
           +KPATATA LTQ M+  +VD+G++P GA+S+ICG +  LLD + + DVV+FTGSA T   
Sbjct: 181 VKPATATAWLTQRMIADVVDAGILPRGALSVICGGSAGLLDQVQAFDVVSFTGSAETAAS 240

Query: 240 LRVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIR 299
           LR  P  V +     +EADSLN  +L  D TPD P F LFI+EVVREMT K+GQKCTAIR
Sbjct: 241 LRAHPAFVVRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIR 300

Query: 300 RIIVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCE 359
           R  VP   ++AV DAL  +L K+ VG+P  + V+MG+LV+  Q  +V   +  L      
Sbjct: 301 RAFVPDTALDAVVDALKTKLAKITVGNPRNDAVRMGSLVSRAQYENVLAGIAALRQEAVL 360

Query: 360 IRLGGQADL----SAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMP--------AQ 407
              G  A L    +A  A   P L     PD    +H  E FGPVA++ P          
Sbjct: 361 AYDGSAAPLIDADAAVAACIAPHLFVVNDPDNATLLHDVEVFGPVASVAPYCVANGAGEL 420

Query: 408 NQRHALQLACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPL 467
            + HA+ LA  G GSL  ++ + D     +   + A +HGR+  ++    +  TGHG+ +
Sbjct: 421 REAHAVDLARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAVSPSVEQSQTGHGNVM 480

Query: 468 PQLVHGGPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISK 511
           P  +HGGPGRAGGGEELGGLRA+  Y +R+A+Q S   + A+++
Sbjct: 481 PMSLHGGPGRAGGGEELGGLRALGFYHRRSAIQASAAAIDAVAQ 524


Lambda     K      H
   0.319    0.134    0.395 

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: 794
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: 681
Length of database: 531
Length adjustment: 37
Effective length of query: 644
Effective length of database: 494
Effective search space:   318136
Effective search space used:   318136
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: 53 (25.0 bits)

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate H281DRAFT_02531 H281DRAFT_02531 Acyl dehydratase

Query= BRENDA::P77455
         (681 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02531 H281DRAFT_02531 Acyl
           dehydratase
          Length = 161

 Score = 60.8 bits (146), Expect = 4e-14
 Identities = 47/132 (35%), Positives = 67/132 (50%), Gaps = 17/132 (12%)

Query: 533 ELQPGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAA 592
           +++ GD  LT   T+TE  +VNFA +SGD++  H+D +AA E+ F  R+ HG   LS A 
Sbjct: 22  DIEAGDYYLTAGVTVTETHVVNFAGVSGDYYDIHVDDVAAQEAGFPGRIAHGLLGLSLAD 81

Query: 593 GLFVDAGVGPVIANYGLESL----RFIEPVKPGDTIQVRLTC--KRKTLKKQRSAEEKPT 646
           GL       PV+   GL +L     F  P+  GD I V +    KR T +  R       
Sbjct: 82  GLKTRC---PVLLK-GLATLGWNWSFRAPLMIGDRIHVDIEVIGKRPTKRPDR------- 130

Query: 647 GVVEWAVEVFNQ 658
           G+    ++V NQ
Sbjct: 131 GIATLRLKVLNQ 142


Lambda     K      H
   0.319    0.134    0.395 

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: 223
Number of extensions: 9
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: 681
Length of database: 161
Length adjustment: 28
Effective length of query: 653
Effective length of database: 133
Effective search space:    86849
Effective search space used:    86849
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory