GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaZ2 in Phaeobacter inhibens BS107

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate GFF3676 PGA1_262p00800 phenylacetic acid degradation protein PaaZ

Query= BRENDA::P77455
         (681 letters)



>lcl|FitnessBrowser__Phaeo:GFF3676 PGA1_262p00800 phenylacetic acid
           degradation protein PaaZ
          Length = 710

 Score =  352 bits (903), Expect = e-101
 Identities = 237/684 (34%), Positives = 347/684 (50%), Gaps = 32/684 (4%)

Query: 4   LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63
           L S ++  W     ++++   A + +    +     D   A  FA   G PALRA+ F +
Sbjct: 11  LQSLIAERWDHCGAQTQVFADAATNQPNAVLAYGSDDGIQAVDFARAVGGPALRALGFQD 70

Query: 64  RAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPD-DT 122
           RA  L+AVA+ L   +   Y  S   GATR D  +D++GGI  L   A    + LP+   
Sbjct: 71  RAQQLRAVARILKDNRAALYRESLTIGATRHDCALDVDGGIARLSALAGQALKSLPNAPV 130

Query: 123 LWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKP 182
           L  ED + P S  G    + +L   SGVA+H+ A + P  G+LE++AP  + G+P I+ P
Sbjct: 131 LHLEDGIGPGSTTG---RQQILAPLSGVALHVTALDNPVSGLLEQIAPALIAGVPCIVCP 187

Query: 183 ATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRV 242
              TA +++ +VK I D  ++P GA+ LI      L+D+L + D ++F G  +T Q LR 
Sbjct: 188 DPVTACVSERLVKMIHDGQILPTGALQLIYNPPLGLVDNLSAGDAISFAGFRSTAQKLRQ 247

Query: 243 QPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRII 302
            P +    +        L+  +LG DV P   E+  F+RE+  E+  +AGQ+  A+RRI+
Sbjct: 248 HPAVATGLVRLQSCETGLSAAILGSDVAPGSQEYQFFLREIRSELILRAGQRRHAVRRIL 307

Query: 303 VPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRL 362
           +P+     V   L   L   +VG P     +MGALV+      VQ+ ++       E+R 
Sbjct: 308 LPRHREAEVLADLSVTLADTIVGVPDDAATQMGALVSRGHLETVQKALD-------ELRH 360

Query: 363 GGQ-------ADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQL 415
           G +         +   GAF  P LL+C +P  TP VH T   GPVAT M   +   A+ L
Sbjct: 361 GAEFVSDPIITPVETGGAFLSPVLLHCAKPANTPDVHQTFVQGPVATAMAYDSLCDAIAL 420

Query: 416 ACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQL----V 471
           A     S    + T D  +A++  A      G+I+I   E A++++   SP P +     
Sbjct: 421 ANLAPCSRYSNVFTNDSPLAQEAAACLTSAEGQIRICGSEMARQAS-ELSPDPSVPRLFA 479

Query: 472 HGGPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYF 531
                +  G E++    AV  YM RT +   P +L A++ +WV GA+   +  HPFRK  
Sbjct: 480 ATHHAQVCGAEDI--RHAVAAYMMRTEIHAPPQLLTALTGRWVEGAETRHNG-HPFRKSL 536

Query: 532 EELQPGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAA-AESIFGERVVHGYFVLSA 590
           E L+ GD L+T  R +TE D+  FA  +GD FYAHMD+ AA +   F +RV HG  V+S 
Sbjct: 537 ETLRIGDQLITETRQITEQDVEQFAHFTGDVFYAHMDREAARSHPFFDDRVAHGQLVVSF 596

Query: 591 AAGLFVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVE 650
           A GL VD   GPV+AN G ++LRF  PV  GD + VR+TCK  T +        P G V 
Sbjct: 597 ANGLLVDPAPGPVLANIGSDNLRFHAPVYFGDCLHVRVTCKEITPR-----ASAPFGDVR 651

Query: 651 WAVEVFNQHQTPVALYSILTLVAR 674
           W   V N     VA + +LTLV +
Sbjct: 652 WDCCVLNACGVVVARFDLLTLVMK 675


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: 1072
Number of extensions: 50
Number of successful extensions: 7
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: 710
Length adjustment: 39
Effective length of query: 642
Effective length of database: 671
Effective search space:   430782
Effective search space used:   430782
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: 54 (25.4 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