GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cup4G11:RR42_RS27915
          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.

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