GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_00370
          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)



>FitnessBrowser__Burk376:H281DRAFT_02531
          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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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