GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF3676
          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 (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