GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Pseudomonas fluorescens FW300-N2E2

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf6N2E2_2873 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)

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



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2873
           Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
          Length = 562

 Score =  243 bits (619), Expect = 2e-68
 Identities = 167/539 (30%), Positives = 263/539 (48%), Gaps = 49/539 (9%)

Query: 52  HQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110
           + G   TYA+L+  +   A  L     L PGDR+ +   N  ++ +      + GL++VN
Sbjct: 45  NMGVTLTYAELERYSAAFAGYLQAHTDLAPGDRIAVQMPNILQYPIAVFGALRAGLIVVN 104

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

Query: 171 KTVV--WIDDEAGQGADE-------PGLLRFTELIARGNAADPRLAQVAAGLQATDPINI 221
                 W+ +       +       P  + F   +  G     +  +V+      D   +
Sbjct: 157 MPTAKGWLVNTMVSKVKKMVPAYSLPQAISFKSALRLGRGQGIKPLKVSLD----DIAVL 212

Query: 222 QFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR----------LCIPVPLYHCFG 271
           Q+T GTTG  KGA LTH N++ N      C+     D           +  P+PLYH + 
Sbjct: 213 QYTGGTTGLAKGAMLTHGNLVANMQQARACLGQLGDDGHPLLREGQEVMIAPLPLYHIYA 272

Query: 272 MVLGNLACF----THGATIVYPND--GFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPR 325
               N  C      H   I  P D  GF     ++ +++ R + L G+ T+F+A +DHP 
Sbjct: 273 FT-ANCMCMMVTGNHNVLITNPRDIGGF-----IKELKNWRFSLLLGLNTLFVALMDHPD 326

Query: 326 FAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSK 385
           F   + S L+     G+       +R  EQ+    IT  YG+TETSPV+  S+       
Sbjct: 327 FKTLDFSNLKVTNSGGTALIKATAERW-EQITGCGITEGYGLTETSPVA--SANPYGGKS 383

Query: 386 RVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGW 445
           R+ TVG   P   +K+++ D G   P+G+RGE C KG  +M GYW     T E +D  GW
Sbjct: 384 RLGTVGMPVPGTLMKVINDD-GVEQPLGERGELCIKGPQIMKGYWNKPEATAEVLDHEGW 442

Query: 446 MHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKY 505
             +GD+A +D +G+V IV R KDM+I  G N+YP EIE+ +  HP+V +  V+GVPD++ 
Sbjct: 443 FRSGDIAVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIEDVVMAHPKVANCAVIGVPDERS 502

Query: 506 GEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
           GE +  +++A+  T  + ++++A+CK     YK+P++I    S PMT  GKI + ++RD
Sbjct: 503 GEAVKLFVVARE-TGVSLEELKAYCKENFTGYKIPKHIVLRDSLPMTPVGKILRRELRD 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: 785
Number of extensions: 36
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 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