GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Phaeo:GFF3354 PGA1_c34070
           long-chain-fatty-acid- CoA ligase IcfB
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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