GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Caulobacter crescentus NA1000

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate CCNA_01017 CCNA_01017 acyl-CoA synthetase

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



>lcl|FitnessBrowser__Caulo:CCNA_01017 CCNA_01017 acyl-CoA synthetase
          Length = 530

 Score =  236 bits (602), Expect = 2e-66
 Identities = 165/525 (31%), Positives = 253/525 (48%), Gaps = 39/525 (7%)

Query: 46  EALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVG 105
           +A+    +GR  T+AQL    +++A+ALL  GL+ GDR+     N+  +  + L  A+ G
Sbjct: 26  DAVAFSFEGRETTFAQLDRHTNQVANALLAAGLSTGDRIAYVGKNSDHYFELLLGAAKAG 85

Query: 106 LVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAA 165
           +V   I       E+ Y +     KL+          ++G  REL         GH+ A 
Sbjct: 86  VVTTPIGWRLAAPEIAYIVGDSEAKLV----------FVG--RELI--------GHVDAV 125

Query: 166 KLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTS 225
                   V I  EA    D      + +  +  +   P        +Q +D     +TS
Sbjct: 126 AAELTHRPVVIAMEAEGAGDYQTFEGWRDAASDVDPHKP--------IQISDIAIQLYTS 177

Query: 226 GTTGFPKGATLTHRNILNNGFFIG----ECMKLTPADRLCIPVPLYHCFGMVLGNLACFT 281
           GTTG PKGA LTH N+L           E  +  P+D   + +P+ H  G   G L    
Sbjct: 178 GTTGRPKGAMLTHHNLLGMRREAAKNPLEWNQWGPSDVSLVAMPVAHIGGTGWG-LVGLI 236

Query: 282 HGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAG 341
           +GA  V   + FDP  VL  ++ +R + +  VP      +  PR  E + S L   +   
Sbjct: 237 NGAKGVVARE-FDPTKVLDFIEKDRISKMFMVPAALQIVVRLPRAREVDYSRLTHILYGA 295

Query: 342 SPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQ---SSTDTPLSKRVSTVGQVQPHLE 398
           +P P ++++  +E      +   YGMTET+           D   +KR+   G   P +E
Sbjct: 296 APIPLDLLRECMEVFGCGFVQ-QYGMTETTGTVVYLPPEDHDPAGNKRMRAAGLPMPGVE 354

Query: 399 VKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEG 458
           +KI+D + G  +P    GE   +  + M GYW  +  T + +D  GW+ TGD   +D +G
Sbjct: 355 LKIID-EAGKSLPPNTVGEVAVRSSANMAGYWKLDEATAKTMDADGWLRTGDAGYLDEDG 413

Query: 459 YVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPG 518
           Y+ I  R+KDM+I GGENIYP E+E  +Y HP V +V V+GVPD K+GE + A +  KPG
Sbjct: 414 YLFIHDRVKDMIISGGENIYPAEVESAVYGHPHVAEVAVIGVPDDKWGEAVKAVVAPKPG 473

Query: 519 TQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563
             P  DDI AF + +IAH+K P+ + F+ + P   +GKI + ++R
Sbjct: 474 VTPDADDIIAFARTRIAHFKAPKSVDFIPALPRNASGKILRRELR 518


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: 709
Number of extensions: 30
Number of successful extensions: 5
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: 578
Length of database: 530
Length adjustment: 36
Effective length of query: 542
Effective length of database: 494
Effective search space:   267748
Effective search space used:   267748
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, 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