GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaK in Pseudomonas putida KT2440

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate PP_4550 PP_4550 long-chain-fatty-acid/CoA ligase

Query= BRENDA::A7KUK6
         (562 letters)



>lcl|FitnessBrowser__Putida:PP_4550 PP_4550
           long-chain-fatty-acid/CoA ligase
          Length = 562

 Score =  190 bits (483), Expect = 1e-52
 Identities = 160/535 (29%), Positives = 247/535 (46%), Gaps = 58/535 (10%)

Query: 46  TYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYT 105
           +Y  L   S  F   L+   + + G+ +A+  PN +  P+ ++G + AG  +   NP YT
Sbjct: 51  SYAELERHSAAFAAWLQQHTDLKPGERIAVQMPNVLQYPIAVFGAMRAGLIVVNTNPLYT 110

Query: 106 VDELAFQLKNSHAKGLV-------TQASVLP---VAREAAKKVG--MPEDRIILIGDQRD 153
             E+  Q K+S A+ LV           VLP   +      K+G  +P  +  L+    D
Sbjct: 111 EREMRHQFKDSGARALVYLNMFGKRVQEVLPDTGIEYLIEAKMGDLLPAAKGWLVNTVVD 170

Query: 154 PDARVKHFTSVRNISGATRYRK-----QKITPAK------DVAFLVYSSGTTGVPKGVMI 202
              ++K       +  A  +++     + ++P        D+A L Y+ GTTG+ KG M+
Sbjct: 171 ---KLKKMVPAYRLPQAVPFKQVLREGRGLSPKPVSLNLDDIAVLQYTGGTTGLAKGAML 227

Query: 203 SHRNIVANIRQQFIAEGEMLSWNGGPDGK-----GDRVL-AFLPFYHIYGLTCLITQALY 256
           +H N+VAN+ Q      +      GPDG+     G  V+ A LP YHIY  T      + 
Sbjct: 228 THGNLVANMLQVLACFSQH-----GPDGQKLLKDGQEVMIAPLPLYHIYAFTANCMCMMV 282

Query: 257 KGYH-LIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGA 315
            G H +++ +  DI  +   +  +R S    +  + + L  HP   + D S+L++ NSG 
Sbjct: 283 TGNHNVLITNPRDIPGFIKELGKWRFSALLGLNTLFVALMDHPGFRQLDFSALKVTNSGG 342

Query: 316 APLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMT 375
             L +   E         I +GYGL+ETSP   +  +      +G+VG  +P     +  
Sbjct: 343 TALVKATAERWEDLTGCRIVEGYGLTETSPVASTNPYGQLAR-LGTVG--IPVAGTAFKV 399

Query: 376 MPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGN 435
           + +DG+E   +  GE GEL +KGP V  GY + PEAT   L  +GWF+TGD+   D  G 
Sbjct: 400 IDDDGNE---LPLGERGELCIKGPQVMKGYWQQPEATAQALDAEGWFKTGDIAVIDPDGF 456

Query: 436 FYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAK 495
             I DR K++I   GF V P E+E  ++ +  + + A IG+  E  G  V +  V R   
Sbjct: 457 TRIVDRKKDMIIVSGFNVYPNEIEDVVMGHPKVANCAAIGVPDERSGEAVKLFVVPR--- 513

Query: 496 SKSSGTSEKDEAARIIK--WLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILK 548
               G    DE     K  +   KV  H  LR      + +P  P GKILRR L+
Sbjct: 514 ---EGGLSVDELKAYCKANFTGYKVPKHIVLR------ESLPMTPVGKILRRELR 559


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: 738
Number of extensions: 27
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 562
Length of database: 562
Length adjustment: 36
Effective length of query: 526
Effective length of database: 526
Effective search space:   276676
Effective search space used:   276676
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: 53 (25.0 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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