Alignments for a candidate for paaZ2 in Sinorhizobium fredii NGR234

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Sinorhizobium fredii NGR234

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_012709127.1 NGR_RS24200 phenylacetic acid degradation bifunctional protein PaaZ

Query= BRENDA::P77455
         (681 letters)



>NCBI__GCF_000018545.1:WP_012709127.1
          Length = 685

 Score =  718 bits (1853), Expect = 0.0
 Identities = 378/683 (55%), Positives = 472/683 (69%), Gaps = 13/683 (1%)

Query: 2   QQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTF 61
           ++L S++ G W  G      +  A +G  +  V S G+D AAAR +  +K  PALR M+F
Sbjct: 9   RRLESYVGGVWTRGAKEGVALLDAATGAPVALVDSTGIDFAAARAYGRDKAGPALRRMSF 68

Query: 62  IERAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDD 121
            ERAAMLKA+A+ L+  K+ FYALS  TGATR DSW+DIEGGIGTLF+YAS G RELP+ 
Sbjct: 69  HERAAMLKALAQALMERKDEFYALSTATGATRTDSWIDIEGGIGTLFSYASKGRRELPNT 128

Query: 122 TLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIK 181
            +  + ++  LS +G F+ARH+LT   GVA+HINAFNFPCWGMLEKLAPT L GMPAI+K
Sbjct: 129 RVLVDGDVETLSSDGTFSARHILTPLEGVAIHINAFNFPCWGMLEKLAPTLLAGMPAIVK 188

Query: 182 PATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLR 241
           PA+ TA LT+ MV+ IV++GL+PEGA+ L+CGS GDLLDH+DSQDVVT TGSA TG+ L+
Sbjct: 189 PASQTAYLTELMVRRIVETGLLPEGAVQLVCGSIGDLLDHVDSQDVVTLTGSAVTGRKLK 248

Query: 242 VQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRI 301
             P IV  S+ FTMEADSLN  VLG D  P   EF LF++EV REMT KAGQKCTAIRR+
Sbjct: 249 THPAIVENSVRFTMEADSLNAAVLGHDAGPGTEEFELFVKEVAREMTAKAGQKCTAIRRV 308

Query: 302 IVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIR 361
           I P+A  +A+  AL  RL KV +G+PA E VKMG L +  QR +V+ ++   LAA  EI 
Sbjct: 309 IAPRAHCDALIAALGERLGKVALGNPADESVKMGPLASLGQREEVRARLRD-LAADAEIV 367

Query: 362 LGGQADL------SAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQL 415
           +G  +          AGAF  P LLYC +P    AVH  EAFGPV+T+MP      A++L
Sbjct: 368 VGDPSSALVVSGDPEAGAFLNPVLLYCDRPAAAGAVHDVEAFGPVSTVMPYDTADEAIEL 427

Query: 416 ACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGP 475
              G GSL  ++ T D +IA + +   A  HGR+ I N  SAK STGHGSPLP LVHGGP
Sbjct: 428 VKRGKGSLVTSVFTNDARIAEELVLGIAPFHGRVMIGNRRSAKSSTGHGSPLPGLVHGGP 487

Query: 476 GRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQ 535
           GRAGGGEELGG+R VKHYMQRTAVQG+P++L+A++ +WV GA+   D  HPFRK   EL+
Sbjct: 488 GRAGGGEELGGMRGVKHYMQRTAVQGAPSLLSAVTGRWVEGAEARVDGEHPFRKSLAELR 547

Query: 536 PGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAA-AESIFGERVVHGYFVLSAAAGL 594
            GD L+T  RT+T  DI +FA  +GD FYAHMD+ AA A   F  RV HGY ++S AAGL
Sbjct: 548 IGDQLVTATRTVTLEDIEHFASFTGDTFYAHMDEEAARANPFFDGRVAHGYLIVSFAAGL 607

Query: 595 FVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVE 654
           FVD   GPV+ANYG+++LR + PV PGDT+QVRLTCK   +  + +AE    G V W   
Sbjct: 608 FVDPAPGPVLANYGVDNLRLLTPVYPGDTLQVRLTCKE--INPRINAEH---GEVRWDCR 662

Query: 655 VFNQHQTPVALYSILTLVARQHG 677
           V NQ    VA Y +LT+VA+  G
Sbjct: 663 VTNQTGATVAGYDVLTMVAKTRG 685


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: 1140
Number of extensions: 47
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: 685
Length adjustment: 39
Effective length of query: 642
Effective length of database: 646
Effective search space:   414732
Effective search space used:   414732
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 Apr 09 2024. 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:

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 2024 update 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