Aligments for a candidate for paaK in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for paaK in Burkholderia phytofirmans PsJN

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate BPHYT_RS15945 BPHYT_RS15945 AMP-binding protein

Query= BRENDA::A7KUK6
         (562 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS15945 BPHYT_RS15945 AMP-binding
           protein
          Length = 520

 Score =  168 bits (426), Expect = 4e-46
 Identities = 149/491 (30%), Positives = 231/491 (47%), Gaps = 41/491 (8%)

Query: 64  LYEW--RKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGL 121
           L EW  R GD + +   NSI   V+++ T         +N   +  EL      +HA   
Sbjct: 64  LREWGVRGGDRVMIVAENSIVQIVLLFATARLDAWALVSNARLSAAEL--DSIRAHA--- 118

Query: 122 VTQASVLPVAREAAKKVGMPEDRIILI-GDQRDPDARVKHFTSVRNISGATRYRKQKITP 180
             Q  ++  A E++    +  +R          PD     +T    +  A      +   
Sbjct: 119 --QPRIVAYATESSADAKLHAERHHAAKAPAFTPDIGAWSYT----VDSAAVAEPVEAAS 172

Query: 181 AKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLP 240
            +  A L+Y++GTTG PKGVM+SHRN++      FIA         GPD   D V A LP
Sbjct: 173 ERQCAALIYTTGTTGAPKGVMLSHRNLL------FIAAISSRLRKVGPD---DVVYAVLP 223

Query: 241 FYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVV 300
             H+YG   +   +L+ G  L ++ +F  E     + + R S    VP +   L +H   
Sbjct: 224 ISHVYGFASVCLGSLHAGATLRLVPRFAPEAVRRALADERVSIFQGVPAMHAKLLEHLQT 283

Query: 301 DKYDLSS--LRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREA 358
             +  S+  LR   SG +PL   L   V S   + +  GYG++E+SPT  S    D   +
Sbjct: 284 HGHAWSAPHLRFAYSGGSPLDAALKAQVESVCGLPLHNGYGMTESSPTV-SHTMLDAPRS 342

Query: 359 MGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSE 418
             SVG ++P ++ +++     G +  +  +G++GEL+++GPNV LGY+ + E T+  ++E
Sbjct: 343 DCSVGEVIPGVEVRFV-----GLDGIDAAQGDIGELWVRGPNVMLGYYRSLEQTRAAVTE 397

Query: 419 DGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIES 478
           DGW +TGD+  QDA G  +I  R KELI   GF V PAE+E  L  +  +   AVIG   
Sbjct: 398 DGWLKTGDLARQDADGALHIVGRSKELIIRSGFNVYPAEVEHVLNAHPQVVQSAVIGRAV 457

Query: 479 ETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNP 538
           E  G+E  +A V          T      A +I     ++A +KR    V  +  +P   
Sbjct: 458 E--GNEEVVAFV-------ELLTGATVTPAELIDCCGERLAPYKR-PAEVKVLAALPAAS 507

Query: 539 SGKILRRILKQ 549
           +GKIL+  L++
Sbjct: 508 TGKILKHRLRE 518


Lambda     K      H
   0.317    0.136    0.410 

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: 586
Number of extensions: 31
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: 562
Length of database: 520
Length adjustment: 35
Effective length of query: 527
Effective length of database: 485
Effective search space:   255595
Effective search space used:   255595
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 preprint on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources