GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Phaeobacter inhibens BS107

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate GFF3354 PGA1_c34070 long-chain-fatty-acid- CoA ligase IcfB

Query= BRENDA::A7KUK6
         (562 letters)



>FitnessBrowser__Phaeo:GFF3354
          Length = 500

 Score =  167 bits (422), Expect = 1e-45
 Identities = 146/487 (29%), Positives = 231/487 (47%), Gaps = 52/487 (10%)

Query: 70  GDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLP 129
           GD +A     S+    +  GT+ AG    P NP YT  E+A+ + ++  +  V      P
Sbjct: 56  GDRVAAQVDKSLAAIQLYLGTVMAGAIFLPLNPAYTEAEVAYFIGDATPRVFVCN----P 111

Query: 130 VAREAAKKVGMPEDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKDVAFLVY 189
           V  E+ + V      + L G+ +   A +         +G   +   +  P+ D+A ++Y
Sbjct: 112 VRHESLRAVAGEATVLTLDGEGQGSLADLA--------AGHAGFEPIERKPS-DLAAILY 162

Query: 190 SSGTTGVPKGVMISHRNIVAN---IRQ--QFIAEGEMLSWNGGPDGKGDRVLAFLPFYHI 244
           +SGTTG  KG M+SH N+ +N   +R   QF AE              D ++  LP +H 
Sbjct: 163 TSGTTGRSKGAMLSHENLYSNSLTLRDYWQFTAE--------------DVLIHALPIFHT 208

Query: 245 YGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYD 304
           +GL      AL  G  ++++  FD E   A + N             LL+      D   
Sbjct: 209 HGLFVATNVALLAGAQVVLLPGFDAEAILAAMPNATALMGVPTFYTRLLVDARLTPDL-- 266

Query: 305 LSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGR 364
            +++R+  SG+APL  E  E   +R    I + YG++ET+ +T S  ++  R A G+VG 
Sbjct: 267 AANMRLFISGSAPLLVETHEQWEARTGHRILERYGMTETNMST-SNPYDGVRVA-GTVGP 324

Query: 365 LMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQT 424
            +P ++A+         +  E+  GE+G L ++GPNVF GY + PE T   L  DGWF T
Sbjct: 325 PLPGVEARVTL------DNAEIPLGEIGVLEVRGPNVFQGYWQMPEKTAEELRPDGWFIT 378

Query: 425 GDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSE 484
           GD+   D+ G   I  R K+L+   GF V P E+E  + D   + + AVIG+     G E
Sbjct: 379 GDLAKIDSNGYVTIVGREKDLVISGGFNVYPKEVETLIDDLPGVLESAVIGVPHPDFG-E 437

Query: 485 VPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILR 544
             +A VV         T E  +AA I   L   +A  K+ +  +  +DE+P+N  GK+ +
Sbjct: 438 AVVAVVV--------PTEEGTDAASIQAALSEHLAKFKQPK-HIALMDELPRNTMGKVQK 488

Query: 545 RILKQKF 551
           + L++ F
Sbjct: 489 KALRETF 495


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: 601
Number of extensions: 26
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: 562
Length of database: 500
Length adjustment: 35
Effective length of query: 527
Effective length of database: 465
Effective search space:   245055
Effective search space used:   245055
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