GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Cupriavidus basilensis 4G11

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 RR42_RS27915 RR42_RS27915 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS27915 RR42_RS27915 acyl-CoA
           synthetase
          Length = 545

 Score =  562 bits (1448), Expect = e-164
 Identities = 289/551 (52%), Positives = 366/551 (66%), Gaps = 24/551 (4%)

Query: 12  LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71
           L K PAN+  LTP+ FL RAA V+  R +++HG     WR TY R RRLAS LA   +G 
Sbjct: 9   LGKNPANHVPLTPIDFLARAASVYGDRLAIVHGPVRQNWRDTYARARRLASGLASLGVGK 68

Query: 72  GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131
           G TVA + PN PAM EAHFGVPM GAVLN +NIRL+A  + F+L H ++ V++ D EF  
Sbjct: 69  GDTVAALLPNTPAMVEAHFGVPMAGAVLNALNIRLDASNLIFMLRHGEARVLLADTEFAD 128

Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191
           +A    ++  E  G      L +V       P+    A + G  +YE  LA+GDP + WQ
Sbjct: 129 VAR---QIANEIPG------LKVVAVLDALGPQD---APAFGETDYERLLASGDPEFAWQ 176

Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251
            PADEW +IAL YTSGTT  PKGVV HHRGA I A+SN L W +   AVYLWTLPMFHCN
Sbjct: 177 MPADEWDAIALNYTSGTTGDPKGVVYHHRGAAINAISNILEWDLPKHAVYLWTLPMFHCN 236

Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAP---KEDTI 308
           GWCFPW++A  +G ++CLR+   K V+ ++    VTH+CAAP+V  A+VNAP   ++   
Sbjct: 237 GWCFPWTIAARAGVNVCLRKFEPKLVFDLMRDEGVTHYCAAPIVHTALVNAPLAWRDGVR 296

Query: 309 LPLPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPET 368
            P    V  M AGA PP +VL  M   GF + H YGL+ETYGP+ VCA + +W SL  E 
Sbjct: 297 GP----VRGMVAGAPPPAAVLAQMEAMGFALTHVYGLTETYGPAAVCAEQDDWASLSQED 352

Query: 369 QAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKET 428
           +A   ARQGVRY    ++ V+D  T +PV +DG+  GEI+FRGN+ MKGYLKN +A +E 
Sbjct: 353 RATKKARQGVRYHLQTEVAVLDPDTMQPVASDGEEIGEIMFRGNICMKGYLKNEKATREA 412

Query: 429 FAGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVAR 488
           FAGGWFH+GD+ V  PD Y++IKDRSKD+IISGGENISSVEVE+ +Y HPAVL  +VVA+
Sbjct: 413 FAGGWFHTGDLGVCTPDGYVKIKDRSKDIIISGGENISSVEVEDAIYRHPAVLAVAVVAQ 472

Query: 489 PDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGK 548
           PD +W E+PCAFV LK        +  A +++  CR  L  + VPK+V FGPLPKT+TGK
Sbjct: 473 PDVKWGETPCAFVELKD-----GASATADELIAHCRTLLAGFKVPKAVYFGPLPKTSTGK 527

Query: 549 IQKHILRTKAK 559
           IQK  LR K K
Sbjct: 528 IQKFELRKKVK 538


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: 926
Number of extensions: 46
Number of successful extensions: 4
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: 545
Length adjustment: 36
Effective length of query: 533
Effective length of database: 509
Effective search space:   271297
Effective search space used:   271297
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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