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_01382 CCNA_01382 long-chain-fatty-acid--CoA ligase

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



>FitnessBrowser__Caulo:CCNA_01382
          Length = 583

 Score =  229 bits (585), Expect = 2e-64
 Identities = 171/538 (31%), Positives = 255/538 (47%), Gaps = 54/538 (10%)

Query: 51  VHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110
           VH+  R  +         +A+ L   G+  GDRV I   N  EW +       +G ++  
Sbjct: 69  VHEDERVNFEAFYRAVTHMAAELESFGVQKGDRVAIVMRNLPEWPVAFYGALSLGAIVTP 128

Query: 111 INPAYRTAEVEYALNKVGCKL-LVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQ 169
           +N  +   E+EY L   G K+ +V + R+              E  G+   HL     P 
Sbjct: 129 LNAWWTGPELEYGLVDSGAKVAIVDVERY--------------ERMGE---HLH--NCPD 169

Query: 170 LKTVVWIDDEAGQGADEPGLLRFTELIARGN----AADPRLAQVAAGLQATDPINIQFTS 225
           LK V      A +    P ++     I   N      +  L  VA  + A D   I +TS
Sbjct: 170 LKRVYV--SRAKEEITHPYVIPLESKIGGANDWAKLDEKPLPTVA--ITADDDATIFYTS 225

Query: 226 GTTGFPKGATLTHRNILNNGFFI-----------GECMKL----TPADRLCIPVPLYH-- 268
           GTTG PKGA  THRNI +N F             GE         P     + VP +H  
Sbjct: 226 GTTGKPKGAIATHRNINSNIFAAAAAGARAFLRRGEAPPQPDPSAPQKGALLSVPFFHAT 285

Query: 269 -CFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFA 327
            CF ++  +L     GA +      +DP   +Q +QDE+ T + GVPT+    ++HP  A
Sbjct: 286 GCFAVLNPSLFA---GAKLAMMRK-WDPERAMQVIQDEKLTQMGGVPTIAWQIIEHPNRA 341

Query: 328 EFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRV 387
            ++LS++      G+P   E+++++ E          +GMTETS  +  +S +     R 
Sbjct: 342 NYDLSSIEAVAYGGAPSAPELVRKIKEIWPKSSPGNGWGMTETSATATSNSAED-YENRP 400

Query: 388 STVGQVQPHLEVKIVDPDTG-AVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWM 446
            + G   P  ++KI+  +     +PIG+ GE   KG  V+ GYW     T +   +G W+
Sbjct: 401 DSCGPAVPVTDLKIMTVEAPYRELPIGEVGELWCKGPQVVRGYWNKPEATAQTFVDG-WV 459

Query: 447 HTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYG 506
            TGDLA +DAEG+  I+ R KDM+IRGGENIY  E+E  LY HP V D  +VGVP +  G
Sbjct: 460 RTGDLARLDAEGFCFIIDRAKDMLIRGGENIYCIEVENCLYDHPAVMDAALVGVPHKTLG 519

Query: 507 EELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVP-RYIRFVTSFPMTVTGKIQKFKIR 563
           EE  A +  KPG + TE ++RAF   ++A +KVP + + +  + P    GKI K +++
Sbjct: 520 EEPAAVVTLKPGAEATEAELRAFVADRLAAFKVPVKVVFWPETLPRNANGKIMKNELK 577


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: 758
Number of extensions: 39
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: 583
Length adjustment: 36
Effective length of query: 542
Effective length of database: 547
Effective search space:   296474
Effective search space used:   296474
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:

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