GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_01017
          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 (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