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_4549 PP_4549 long-chain-fatty-acid/CoA ligase

Query= BRENDA::D3GE78
         (556 letters)



>lcl|FitnessBrowser__Putida:PP_4549 PP_4549
           long-chain-fatty-acid/CoA ligase
          Length = 565

 Score =  197 bits (500), Expect = 1e-54
 Identities = 156/524 (29%), Positives = 247/524 (47%), Gaps = 43/524 (8%)

Query: 46  LTTHDLRLWSQRLAAGLRK-SGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTF 104
           +T  +L   S   AA L++ + L+ GDR+ +   N L +PV   G + AG I    NP +
Sbjct: 50  ITYGELYALSGAFAAWLQQHTDLKPGDRIAVQLPNVLQYPVAVFGAMRAGLIVVNTNPLY 109

Query: 105 VARELAYQLQDSGATYLLCASNSLETGLEAAKQAKLPQ------------------SHIF 146
            ARE+ +Q  DSGA  L+C +N      +   + ++                    + + 
Sbjct: 110 TAREMEHQFNDSGAKALVCLANMAHLAEKVVPKTQVRHVIVTEVADLLPPLKRLLINSVI 169

Query: 147 AYDTSIYDGVTNPQKGCAYWSDLLASEEEGAAFTWDELSTPALSSTTLALNYSSGTTGRP 206
            Y   +      PQ     ++D LA    G      E +  A  +    L Y+ GTTG  
Sbjct: 170 KYVKKMVPAYNLPQ--AVRFNDALAL---GKGQPVTEANPQA--NDVAVLQYTGGTTGVA 222

Query: 207 KGVEISHRNYVANMLQYCHT---ASLHPDYKARLERSRWLCFLPMYHAMAQNIF-IAAAL 262
           KG  ++HRN VANMLQ C     ++LH   +  +        LP+YH  A     +A  L
Sbjct: 223 KGAMLTHRNLVANMLQ-CRALMGSNLHEGCEILITP------LPLYHIYAFTFHCMAMML 275

Query: 263 YRATPVYIMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGA 322
                V I +  D   M++   +++ + F+ +  + VAL  + A    D S++++  SG 
Sbjct: 276 IGNHNVLISNPRDLPAMVKELGKWKFSGFVGLNTLFVALCNNEAFRALDFSALKITLSGG 335

Query: 323 APLGREVCEEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEISTSASVGELNANCEAKI 382
             L   V E  + +       I +G+GMTE T  V   NP+E +   ++G    +   K+
Sbjct: 336 MALQLSVAERWKAVTGCA---ICEGYGMTE-TSPVAAVNPSEANQVGTIGIPVPSTLCKV 391

Query: 383 MFDGVEVKERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHV 442
           + D          GEL V+ P VMKGYW+ E AT E    +GWL TGDIA +  DG   +
Sbjct: 392 IDDAGNELPLGEVGELCVKGPQVMKGYWQREDATAEILDSEGWLKTGDIAVIQADGYMRI 451

Query: 443 VDRMKELIKVKGNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSAT 501
           VDR K++I V G  V P ELE +L   P +   A IGV    + E  + ++V++PG + T
Sbjct: 452 VDRKKDMILVSGFNVYPNELEDVLAALPGVLQCAAIGVPDEKSGEVIKVFIVVKPGMTVT 511

Query: 502 ANEIAHYLDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQ 545
             ++  ++   V+ +K +   + F +++P    GKILR +LR++
Sbjct: 512 KEQVMEHMRANVTGYK-VPRHIEFRDSLPTTNVGKILRRELRDE 554


Lambda     K      H
   0.319    0.134    0.403 

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: 655
Number of extensions: 26
Number of successful extensions: 4
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: 556
Length of database: 565
Length adjustment: 36
Effective length of query: 520
Effective length of database: 529
Effective search space:   275080
Effective search space used:   275080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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, 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