GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_03315
          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.

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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