GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS15945
          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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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