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_RS25360 RR42_RS25360 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>FitnessBrowser__Cup4G11:RR42_RS25360
          Length = 554

 Score =  543 bits (1400), Expect = e-159
 Identities = 278/548 (50%), Positives = 363/548 (66%), Gaps = 19/548 (3%)

Query: 12  LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71
           L +  AN+  LTPL FLDR A  +P R ++IHG    +W+ T +RCR+LASAL  R +G 
Sbjct: 10  LDRRAANHMPLTPLHFLDRCAEQYPDRTAIIHGPVRQSWKVTRERCRQLASALVKRGVGR 69

Query: 72  GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131
           G TV+I+APN PAM EAH G+P+ GAVLN +N RL+A  V F+++H +  V+ VD+EF  
Sbjct: 70  GDTVSILAPNTPAMVEAHHGIPLSGAVLNAINCRLDADGVRFIVAHGECKVLFVDREFSA 129

Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTC-APESLNRALSKGAIEYEDFLATGDPNYPW 190
           LA ++L+ +          PL+I I D    A E +      GA+EYE FL  GD ++P 
Sbjct: 130 LAAEALQGLPNA-------PLVIDIADALAPAGEPI------GAMEYEQFLREGDIDFPG 176

Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250
             P DEW +IAL YTSGTT+ PKGVV  HRGAY+M++     WGM     YLWTLPMFH 
Sbjct: 177 VWPDDEWNAIALNYTSGTTSDPKGVVPSHRGAYLMSMLQLTDWGMPRAPKYLWTLPMFHA 236

Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310
           NGWCF W++   +GT +CLR+VTA  ++S I  Y   HFCAAP+VL+++  A +E+   P
Sbjct: 237 NGWCFSWAVTAAAGTHVCLRKVTAANIFSAIEAYGADHFCAAPIVLSSLATATQEER-RP 295

Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370
             H V + TAG+ PP SVL ++ ++GF V H YG++E  G        P W+    + +A
Sbjct: 296 FSHVVRIRTAGSPPPASVLKAVIEQGFDVEHVYGITEASGTPVSSYANPAWNEKSGDEKA 355

Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430
           +L ARQG R  G+E L V D  T + VP DG T GE++ RGN+VMKGYLKNPEA +  FA
Sbjct: 356 RLMARQGNRAAGLEGLRVADPDTMESVPWDGTTQGELLLRGNIVMKGYLKNPEATEAAFA 415

Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490
           GGWFH+GD+AV HPD Y++I DRSKDVIISGGENISSVEVE+V++ HPAVL A+VVA+P 
Sbjct: 416 GGWFHTGDLAVVHPDGYVQITDRSKDVIISGGENISSVEVEDVLHQHPAVLIAAVVAQPH 475

Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQ 550
            +W ESPCAF+ LK+      +     +I+ FCR +L  Y  P  VV+G LPKT TGKIQ
Sbjct: 476 PKWGESPCAFIELKNGVAAPTE----AEIIAFCRSRLAHYKCPTRVVYGALPKTGTGKIQ 531

Query: 551 KHILRTKA 558
           K+ LR  A
Sbjct: 532 KYRLRALA 539


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: 906
Number of extensions: 39
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: 554
Length adjustment: 36
Effective length of query: 533
Effective length of database: 518
Effective search space:   276094
Effective search space used:   276094
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:

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