Alignments for a candidate for paaZ2 in Ruegeria conchae TW15

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Ruegeria conchae TW15

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_010437890.1 G7G_RS0102290 phenylacetic acid degradation bifunctional protein PaaZ

Query= BRENDA::P77455
         (681 letters)



>NCBI__GCF_000192475.1:WP_010437890.1
          Length = 674

 Score =  656 bits (1692), Expect = 0.0
 Identities = 351/681 (51%), Positives = 453/681 (66%), Gaps = 16/681 (2%)

Query: 1   MQQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMT 60
           + Q++SF +GTW +    +R I  AI+G       +  LD+ A   +A   G PALR +T
Sbjct: 3   LHQISSFAAGTWVAPGEGARTIASAITGAPFASAGNTALDVQAMLDYARNTGGPALRKLT 62

Query: 61  FIERAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPD 120
           F +RA MLKA+A+ L + K+  Y LS +TGAT+ D  +DI+GGIGT+F +AS G RE+PD
Sbjct: 63  FHDRARMLKALAQELSAHKQALYDLSFETGATQKDHLIDIDGGIGTMFVFASKGRREMPD 122

Query: 121 DTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAII 180
             ++ + ++  LS+ G F  +H+ T   GVAVHINAFNFP WGMLEKLAPT L G+PAI+
Sbjct: 123 AQVYLDGDIEQLSRNGTFLGQHICTPLQGVAVHINAFNFPVWGMLEKLAPTLLAGVPAIV 182

Query: 181 KPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQML 240
           KPAT +  +T+  V+ I+DSG++P GA+ L+ G  GD+LDHL  QDVV+FTGSA T   L
Sbjct: 183 KPATNSCYVTELAVRIILDSGILPAGALQLVSGGLGDMLDHLSCQDVVSFTGSANTALKL 242

Query: 241 RVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRR 300
           R  P I+  S+ F  E DSLN  +LG D  P  PEF LF++EV REMTTKAGQKCTAIRR
Sbjct: 243 RQTPAILQNSVRFVAEQDSLNASILGRDAEPGTPEFDLFVKEVSREMTTKAGQKCTAIRR 302

Query: 301 IIVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEI 360
           II P + V+AV  AL  RL K+ +GDP  E  +MGALV+  Q+ADV EK N++   G E 
Sbjct: 303 IIAPDSQVDAVISALSERLAKITIGDPRAETTRMGALVSNGQKADVLEKANLI---GQEA 359

Query: 361 -RLGGQADL-----SAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQ 414
            R+ G  D         GAF PP L +C  PD+   VH TEAFGPV+TLM  ++  HA+ 
Sbjct: 360 ERVYGNPDAFDLHGPETGAFVPPMLFHCADPDKAQRVHDTEAFGPVSTLMGYRDLDHAVA 419

Query: 415 LACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGG 474
           LA  G GSL  +L+T D ++AR  +  AA  +GRI I +  S  ESTGHGSPLP +VHGG
Sbjct: 420 LANRGQGSLVTSLITHDTEVARDVVMGAAAYNGRIYINDRNSMAESTGHGSPLPHMVHGG 479

Query: 475 PGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEEL 534
           PGRAGGGEE+GG+R VKHYMQRTA+QGSP ML++I  +WV G+   +   HPF + F EL
Sbjct: 480 PGRAGGGEEMGGVRGVKHYMQRTAIQGSPRMLSSIGTKWVTGSPEIQGPAHPFTRKFGEL 539

Query: 535 QPGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAES-IFGERVVHGYFVLSAAAG 593
           Q G++L T  R +T  DI +FA  +GD FYAHMD+ AAA +  F  RV HGY +LS AAG
Sbjct: 540 QVGETLHTASRVITLEDIEHFANFTGDTFYAHMDEEAAARNPFFPGRVAHGYLLLSFAAG 599

Query: 594 LFVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAV 653
           LFV+   GPV+AN GL+ LRF++PV  GD+I+VRLT K+KT +          G V W V
Sbjct: 600 LFVEPNEGPVLANTGLDGLRFMKPVVAGDSIKVRLTVKQKTPRND------DYGEVRWHV 653

Query: 654 EVFNQHQTPVALYSILTLVAR 674
            + NQ   PVA Y +LT+ AR
Sbjct: 654 SLTNQDDEPVAEYELLTMNAR 674


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: 1068
Number of extensions: 38
Number of successful extensions: 4
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: 674
Length adjustment: 39
Effective length of query: 642
Effective length of database: 635
Effective search space:   407670
Effective search space used:   407670
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 24 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources