GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Erythrobacter gangjinensis K7-2

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_047007498.1 AAW01_RS06755 AMP-binding protein

Query= curated2:O93730
         (670 letters)



>NCBI__GCF_001010925.1:WP_047007498.1
          Length = 542

 Score =  116 bits (291), Expect = 2e-30
 Identities = 145/524 (27%), Positives = 211/524 (40%), Gaps = 54/524 (10%)

Query: 116 TDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITLYLPMVPELPITMLAAWRIGAITSV 175
           T  R+ TY +L  +  R+A      F  + G+++ ++ P +PE  +   AA   G     
Sbjct: 49  TTGRRWTYAELLHDAERMAKGFAARF--QPGERVAVWGPNIPEWVLVEYAAALAGLTLVT 106

Query: 176 VFSGFSADALAERINDSQSRIVITADGFWRRGRVVRLKEVVDAALEKATGVESVIVLPRL 235
           V   +    L   +  S S  +     F  RG    +K +     E    +  ++     
Sbjct: 107 VNPAYQKRELDFVLRQSNSAALFLISEF--RGNP--MKSIAQGVAEDLPTLREIV----- 157

Query: 236 GLKDVPMTEGRDYWWNKLMQGIPPNAYIEPE----PVESEHPSFILYTSGTTGKPKGIVH 291
            ++D                    + Y +P      V++  P+ I YTSGTTG PKG+V 
Sbjct: 158 DMQD------------------EASLYTDPSGSLPDVDTNDPAQIQYTSGTTGFPKGVVL 199

Query: 292 DTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSYVVLGPLLMGATEVIYEGAPDY 351
                  +    +K V D+  +        +    G S  VLG L  G            
Sbjct: 200 SHRNLTNNARLFVK-VGDLPKNLSTIGLTPLFHTMGCSMGVLGSLQSGGAYCPLLAF--- 255

Query: 352 PQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKHDLSTLRIIHSVGEPINPEAWR 411
             P     IIER  V+     PT     +   +  PR  DLS+L II   G  + PE  R
Sbjct: 256 -DPGAALDIIEREKVSWTICVPTMAVAMVAAQKAQPR--DLSSLEIIGMGGAMVAPELAR 312

Query: 412 WAYRVLGNEK-VAFGSTWWMTETGGIVISHAPGLYLVPMKPGTNGPPLPGFEVDVVDE-N 469
                LG +  VA+G T    E+  ++ S  P      +   T G P  G EV +VD   
Sbjct: 313 AVEATLGAKALVAYGQT----ESSPLITSGRPTDDFEDIVT-TIGQPALGCEVAIVDAAT 367

Query: 470 GNPAPPGVKGYLVIKKPWPGMLHGIWGDPERYIKTYWSRFPGMFYAGDYAIKDKDGYIWV 529
           G   P    G  +  + +  ML G   +PE   +T      G    GD    D  GY+ +
Sbjct: 368 GEVLPCDTVGE-IRSRSYATML-GYNDNPEATAETVTG--DGWLCTGDLGTMDDRGYVKI 423

Query: 530 LGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGVPDAIKGEVPIAFVVLKQGVAPS 589
            GR  E+I   G  L   E+E+ L+ HPA+AE AVVGVPD + GE   AF+ ++ G    
Sbjct: 424 TGRVKEMIIRGGENLFPAEIENVLLEHPAIAECAVVGVPDDVLGEAVAAFIRVQDGAEFD 483

Query: 590 DELRKELREHVRRTIGPIAEPAQIFFVTKLPKTRSGKIMRRLLK 633
            +     + HVR  I P   PA    VT+ P T SGKI +  L+
Sbjct: 484 PD---AFKAHVRSQIAPQKCPAYWTQVTEWPLTGSGKIRKFQLR 524


Lambda     K      H
   0.319    0.138    0.440 

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: 948
Number of extensions: 63
Number of successful extensions: 4
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: 670
Length of database: 542
Length adjustment: 37
Effective length of query: 633
Effective length of database: 505
Effective search space:   319665
Effective search space used:   319665
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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