GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Pseudomonas fluorescens FW300-N2E3

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate AO353_03315 AO353_03315 long-chain fatty acid--CoA ligase

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_03315 AO353_03315 long-chain
           fatty acid--CoA ligase
          Length = 562

 Score =  251 bits (642), Expect = 4e-71
 Identities = 172/541 (31%), Positives = 265/541 (48%), Gaps = 53/541 (9%)

Query: 52  HQGRRYTYAQLQTEAHRLASALLGM-GLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110
           + G   TYA+L+  +   A  L     L PGDR+ +   N   + +      + GL++VN
Sbjct: 45  NMGVTLTYAELERYSAAFAGYLQTQTDLLPGDRIAVQMPNVLHYPIAVFGALRAGLIVVN 104

Query: 111 INPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQL 170
            NP Y   E+ +     G + LV +  F        ++E+ P+ + Q   +L  AK+  L
Sbjct: 105 TNPLYTAREMRHQFKDSGARALVYLNMFGQK-----VQEVLPDTEIQ---YLIEAKMGDL 156

Query: 171 ---------KTVVWIDDEAGQGADEPGLLRFTELI--ARGNAADPRLAQVAAGLQATDPI 219
                     TVV    +     D P  + F   +   RG +  P+       +   D  
Sbjct: 157 MPTAKGWLINTVVDKVKKMVPTYDLPQAISFKSALRLGRGQSIKPQ------NVSLDDVA 210

Query: 220 NIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR----------LCIPVPLYHC 269
            +Q+T GTTG  KGA LTH N++ N      C+    +D           +  P+PLYH 
Sbjct: 211 VLQYTGGTTGLAKGAMLTHGNLVANMQQARACLGQFGSDGKPLLREGQEVMIAPLPLYHI 270

Query: 270 FGMVLGNLACF----THGATIVYPND--GFDPLTVLQTVQDERCTGLHGVPTMFIAELDH 323
           +     N  C      H   I  P D  GF     ++ +++ R + L G+ T+F+A +DH
Sbjct: 271 YAFT-ANCMCMMVTGNHNVLITNPRDIAGF-----IKELKNWRFSALLGLNTLFVALMDH 324

Query: 324 PRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPL 383
           P F   + S+L+     G+       +R  EQ+    IT  YG+TETSPV+C +      
Sbjct: 325 PNFKTLDFSSLKLTNSGGTALVKATAERW-EQITGCRITEGYGLTETSPVACTNPYGD-- 381

Query: 384 SKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEG 443
             R+ TVG   P   +K+++ D G   P+G+RGE C KG  +M GYW     T E +D  
Sbjct: 382 KSRIGTVGLPVPGTTLKVINDD-GVEQPLGERGELCIKGPQIMKGYWQKPEATAEVLDAD 440

Query: 444 GWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQ 503
           GW  +GD+A +D +G+V IV R KDM+I  G N+YP EIE+ +  HP+V +  V+GVPD+
Sbjct: 441 GWFKSGDIAVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIEDVVMAHPKVANCAVIGVPDE 500

Query: 504 KYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563
           + GE +  +++A+      E +++A+CK     YKVP++I    S PMT  GKI + ++R
Sbjct: 501 RSGEAVKLFVVAREAGISLE-ELKAYCKENFTAYKVPKHIVLRESLPMTPVGKILRRELR 559

Query: 564 D 564
           D
Sbjct: 560 D 560


Lambda     K      H
   0.320    0.136    0.412 

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: 790
Number of extensions: 38
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: 578
Length of database: 562
Length adjustment: 36
Effective length of query: 542
Effective length of database: 526
Effective search space:   285092
Effective search space used:   285092
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 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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