Alignments for a candidate for paaZ2 in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Pseudarthrobacter sulfonivorans Ar51

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_058931418.1 AU252_RS15050 phenylacetic acid degradation bifunctional protein PaaZ

Query= BRENDA::P77455
         (681 letters)



>NCBI__GCF_001484605.1:WP_058931418.1
          Length = 700

 Score =  599 bits (1544), Expect = e-175
 Identities = 333/695 (47%), Positives = 445/695 (64%), Gaps = 27/695 (3%)

Query: 1   MQQLASFLSGTW---QSGRGRSRL-IHHAISGEALWEVTSEGLDMAAARQFAIEKGAPAL 56
           +Q + SF+  +W    +G   S + +  A +GE L +V+++GLD+AA   +    G   L
Sbjct: 12  VQTVPSFVQDSWWTPDAGSAASAVPVRDASTGEVLAKVSTDGLDLAAVVDYGRTTGQTEL 71

Query: 57  RAMTFIERAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSR 116
             +TF +RA  LK +A++L + +E FY  SAQTGAT+ DS +DI+GGIG LFT+ S G R
Sbjct: 72  GKLTFHQRALKLKELAQYLNARREHFYTFSAQTGATKIDSMIDIDGGIGVLFTFGSKGRR 131

Query: 117 ELPDDTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGM 176
           ELP+  +  +  +  LSK+G F A H+ T   GVAV INAFNFP WGMLEKLAP ++ G+
Sbjct: 132 ELPNSQVVVDGPMEVLSKDGSFVAEHIYTRIPGVAVQINAFNFPVWGMLEKLAPAFIAGV 191

Query: 177 PAIIKPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAAT 236
           P I+KPAT T  +  A+VK+I++S ++P+G++ LI GS   LLD LD +D+V FTGSA+T
Sbjct: 192 PIIVKPATPTGYVAAAVVKAIIESNILPKGSLQLISGSVRGLLDVLDYRDLVAFTGSAST 251

Query: 237 GQMLRVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCT 296
              L+  PN+V   + FT E DSLN  +LG D     PEF  FI+ VV EMT KAGQKCT
Sbjct: 252 ALSLKSHPNVVQGGVRFTSETDSLNAAILGPDAVEGTPEFDAFIKSVVTEMTVKAGQKCT 311

Query: 297 AIRRIIVPQALVNAVSDALVARL-QKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLA 355
           +IRR IVP  LV AV  A+  R+ ++VV+GDP  +GV MGAL + EQ  DV+  V  +L 
Sbjct: 312 SIRRAIVPDELVPAVIAAVGRRVDERVVLGDPRADGVTMGALASLEQLTDVRAAVQSMLD 371

Query: 356 AGCEI-----------RLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLM 404
           AG E+             GG   +  AGAF  P +L      ET A+H+ EAFGPVA+++
Sbjct: 372 AGGELAYGTLDSPSVTSAGGATGVVDAGAFMSPVVLSWADA-ETDAIHSLEAFGPVASVI 430

Query: 405 PAQNQRHALQLACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHG 464
             ++   A++LA  GGGSL  ++ T DP +AR+ +   A  HGR+ +LN E A+ STGHG
Sbjct: 431 GYKDLPDAVRLAARGGGSLVASVCTNDPAVARELVTGIAAHHGRVLMLNREDARSSTGHG 490

Query: 465 SPLPQLVHGGPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGA----KVE 520
           SP+P LVHGGPGRAGGGEELGG+R+V H+MQRTA+QGSP ML A++  W  GA     VE
Sbjct: 491 SPVPHLVHGGPGRAGGGEELGGIRSVMHHMQRTAIQGSPNMLTAVTGLWHAGADRNFTVE 550

Query: 521 EDRIHPFRKYFEELQPGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAA-AESIFGE 579
            +  HPFRK    L+ GD++ +  R ++ ADI  FA  +GD FYAH ++ AA A   F  
Sbjct: 551 TEGTHPFRKSLASLRIGDAVRSDLRQVSLADISAFANSTGDTFYAHTNQEAAEANPFFPG 610

Query: 580 RVVHGYFVLSAAAGLFVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQR 639
            V HGY +LS AAGLFV+   GPV+ANYGLE+LRFI PV  GD+I+V LT K+ T +   
Sbjct: 611 IVAHGYLLLSWAAGLFVEPAPGPVLANYGLENLRFITPVAAGDSIRVTLTAKKITPR--- 667

Query: 640 SAEEKPTGVVEWAVEVFNQHQTPVALYSILTLVAR 674
             E    G V W   + NQ+   VA Y +LTLV +
Sbjct: 668 --ETDEYGEVAWDALLTNQNDDIVATYDVLTLVEK 700


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: 1075
Number of extensions: 39
Number of successful extensions: 6
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: 700
Length adjustment: 39
Effective length of query: 642
Effective length of database: 661
Effective search space:   424362
Effective search space used:   424362
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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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