GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Rhodococcus qingshengii djl-6-2

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_030535166.1 C1M55_RS25270 AMP-binding protein

Query= SwissProt::Q8VZF1
         (569 letters)



>NCBI__GCF_002893965.1:WP_030535166.1
          Length = 534

 Score =  439 bits (1130), Expect = e-127
 Identities = 241/546 (44%), Positives = 317/546 (58%), Gaps = 26/546 (4%)

Query: 15  IPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGPGST 74
           + AN T L+PL FL+R+A V P R +V+HG R Y++R+  D    LA  L +R I PG  
Sbjct: 7   VAANNTPLSPLRFLERSAAVFPERTAVVHGDRTYSYREFGDEVAALARVLRER-IQPGDR 65

Query: 75  VAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFTLAE 134
           VA +APN+P M  AHF VP+ G VL  +N RL  P + ++L HS ++++ VD EF     
Sbjct: 66  VAYLAPNVPEMLFAHFAVPLAGGVLIALNSRLAGPELEYILDHSGTTILFVDSEFVGSVT 125

Query: 135 DSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATG----DPNYPW 190
            S      KA     R + + I D T     +   +  G  +Y D +A G    D    W
Sbjct: 126 SS------KANVGSLREI-VEIPDSTVPYPDVPTGIVTG--QYADLIAEGEALSDQPLHW 176

Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250
               DE Q IA+ YTSGTT  PKGV+  HRGAY+ +L      G      YLWTLPMFHC
Sbjct: 177 GVD-DEQQCIAINYTSGTTGKPKGVMYSHRGAYLNSLGETFHNGFDGATKYLWTLPMFHC 235

Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310
           NGWC PW++   +GT ICLR V A  ++  I    VTH C AP V + I +A +   +  
Sbjct: 236 NGWCTPWAVTQAAGTHICLRAVRADAIWDAIDNLGVTHLCGAPTVCSTIADADQAHKV-- 293

Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370
               + + TAGA P P+++  +   G  V H YGL+E YGP T+C ++  WD  P   +A
Sbjct: 294 --DALRITTAGAPPSPTIIGKLEDIGVTVVHVYGLTEVYGPYTICEYQEAWDDKPQSERA 351

Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430
            L +RQGV     E   V+D +    VPADG+T GEIV RGN VM GY ++  A  E FA
Sbjct: 352 ALLSRQGVGMVQAENARVVDAEMND-VPADGQTMGEIVLRGNNVMLGYYRDEAATAEAFA 410

Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490
           GGWFHSGD+ V HPD YI++KDR+KD+IISGGENIS+VEVE  +  HPAV++ +VV  PD
Sbjct: 411 GGWFHSGDLGVMHPDGYIQLKDRAKDIIISGGENISTVEVEQAIMSHPAVIDVAVVGVPD 470

Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFG-PLPKTATGKI 549
           E+W E P AFV L    +       A+DI++  R  L  Y VP+ +VF   LP+T TGK+
Sbjct: 471 EKWGERPKAFVVLGKGLQAS-----AEDIVEHTRTLLAGYKVPRDIVFPLDLPRTPTGKV 525

Query: 550 QKHILR 555
            K  LR
Sbjct: 526 LKFQLR 531


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: 822
Number of extensions: 37
Number of successful extensions: 7
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: 534
Length adjustment: 36
Effective length of query: 533
Effective length of database: 498
Effective search space:   265434
Effective search space used:   265434
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.

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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