GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Sphingobium czechense LL01

Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate WP_082679212.1 V473_RS18440 AMP-binding protein

Query= SwissProt::Q8VZF1
         (569 letters)



>NCBI__GCF_001046645.1:WP_082679212.1
          Length = 622

 Score =  165 bits (417), Expect = 6e-45
 Identities = 157/515 (30%), Positives = 228/515 (44%), Gaps = 47/515 (9%)

Query: 52  QTYDRCRRLASALADRSIGPGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTV 111
           Q +++  R    L    IGPG  VA+  P       A  G+   GAVL  V     A  +
Sbjct: 140 QLHEQGLRFGEHLRAHGIGPGDIVAVQLPAWIEWMIAAVGIAHAGAVLLPVVSIYGAKEL 199

Query: 112 AFLLSHSQSSVIMVDQEFFTLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALS 171
            F+L+ S + +I V  + +  A+ +  L E   G        ++IGD   AP        
Sbjct: 200 RFILAQSGAKLI-VTPDRWRKADYAQTLAE--VGRLPALATHVMIGD--AAP-------- 246

Query: 172 KGAIEYEDFLA--TGDPNYPWQPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSN 229
            G + +E  LA     P  P  P A       L YTSGTTA PKGV   H    I++  +
Sbjct: 247 -GTVPWEAMLAPIAVGPAAPRSPDA----LALLVYTSGTTADPKGV--KHSARTILSEID 299

Query: 230 PLIWGMQD--GAVYLWTLPMFHCNGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVT 287
            + W  +D    V     P  H  G        V     + + Q    E   ++ KY++ 
Sbjct: 300 AVAWSRRDLGAEVAFCPWPPGHVAGALQLMRFLVTGTPVVLMDQWEPGEAAMLVEKYRIV 359

Query: 288 HFCAAPVVLNAIVNAPKEDTILPLPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSE 347
                P  L+ +++A + D    L      M   A  PP+++   + +G +    YG SE
Sbjct: 360 SSSFTPFHLSGLLDAAERDG-RDLSSLRSCMVGAAPVPPTLITRCSAQGLKTYRCYGSSE 418

Query: 348 TYGPSTVCAWKPEWDSLPPETQAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEI 407
               +T           P +   K    +G+   G E LD +D   G+ VP   +  GE+
Sbjct: 419 HPTVTT---------GHPDDIMEKRLTTEGLPMRGTE-LDFVDDD-GQRVPEGME--GEL 465

Query: 408 VFRGNMVMKGYLKNPEANKETFAGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISS 467
           V RG  +  GYL +   +     GGWF +GDI     D ++ I DR KDVII GGENISS
Sbjct: 466 VVRGPELFLGYLDDSLNSAAFLPGGWFRTGDIGRLDQDGFLMITDRKKDVIIRGGENISS 525

Query: 468 VEVENVVYHHPAVLEASVVARPDERWQESPCAFVTLKSDYE---KHDQNKLAQDIMKFCR 524
            EVE++++ HPA+ EA+VVA PDER  E  CA+V  +       +  +   AQ      R
Sbjct: 526 REVEDLLFAHPAIAEAAVVAAPDERMGEIVCAYVVPRPGASVDLESVRTHFAQ--AGIAR 583

Query: 525 EKLPAYWVPKSVVFGPLPKTATGKIQKHILRTKAK 559
           +K P     + +V    P+ +TGKI KH LR +A+
Sbjct: 584 QKTP----ERLIVVDDFPRNSTGKILKHELRAQAR 614


Lambda     K      H
   0.319    0.134    0.422 

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: 902
Number of extensions: 49
Number of successful extensions: 5
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: 569
Length of database: 622
Length adjustment: 37
Effective length of query: 532
Effective length of database: 585
Effective search space:   311220
Effective search space used:   311220
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 24 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