GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Pseudomonas fluorescens FW300-N2E3

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate AO353_19945 AO353_19945 acetyl-CoA synthetase

Query= SwissProt::P39062
         (572 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_19945 AO353_19945 acetyl-CoA
           synthetase
          Length = 588

 Score =  484 bits (1246), Expect = e-141
 Identities = 262/568 (46%), Positives = 346/568 (60%), Gaps = 24/568 (4%)

Query: 26  DWAEAEKHFSWHET---------GKLNAAYEAIDRHAESFRKNKVALYYKDAKRDE-KYT 75
           D  +A + FSW            G LN AYEA+DRHAE   +   AL   D        +
Sbjct: 22  DSVQAREGFSWQGEASALAGLPGGGLNLAYEAVDRHAEGKHRRHTALRILDRNGGRCDIS 81

Query: 76  FKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFME 135
           +  +   SNR  NVL+  G V  G+R+F+   R  ELY  +LG +K+G +  PLF AF  
Sbjct: 82  YARLSLLSNRFANVLKTLG-VVPGERLFVLCGRGLELYLGVLGGLKLGCVVSPLFCAFGP 140

Query: 136 GAVKDRLENSEAKVVVTTPELLERIPV----DKLPHLQHVFVVGGEAESGTNI---INYD 188
             ++ RL   E  V++T+ E L R  V    ++LP L+HV +   E  + T +   ++  
Sbjct: 141 EPIETRLRLGEGSVLLTS-ETLYRHKVAAIRERLPALKHVLLYDEEGGNTTPVEGTLSLH 199

Query: 189 EAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEED 248
                 +   +I         LLH+TSG+TGTPKGVLHVH A++    TGK+ LDL  +D
Sbjct: 200 RLLANATDHFEIAHTTADSPALLHFTSGTTGTPKGVLHVHGAVLTHRVTGKYALDLHPDD 259

Query: 249 IYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFR 308
           IYWC+ADPGWVTGT YGI AP L G T+V+ G  F  E WY T+E+  V VWY+APTA R
Sbjct: 260 IYWCSADPGWVTGTSYGIIAPLLLGVTSVVEGREFDAERWYRTLEKQQVTVWYTAPTAIR 319

Query: 309 MLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICN 368
           +LM AG E+A  +    LR + SVGEPLNPE + WG +V    IHD WW TETG  +I N
Sbjct: 320 LLMKAGAELAHSHRFPCLRFIASVGEPLNPEAVWWGQEVLGLPIHDNWWQTETGGIMIAN 379

Query: 369 YPCMDIKPGSMGKPIPGVEAAIV----DNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPE 424
              M IKPGSMGKP+PGVEAA+V      + + L    +G LA+K+ WP+M  T     E
Sbjct: 380 TVAMTIKPGSMGKPLPGVEAAVVVRGAAGELDYLGDNEVGELALKQPWPAMFRTYLGQEE 439

Query: 425 KYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAE 484
           +Y   F+  GWY+SGD    D +GY+WF GR DDVI ++G  +GPFEVES L+EHPA+AE
Sbjct: 440 RYRQCFV-AGWYLSGDLVRRDADGYYWFIGRSDDVIKSAGHLIGPFEVESSLMEHPAVAE 498

Query: 485 AGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPK 544
           A VIGKPDP+ GE +K F++L+ GF  S  L +E+    ++ L A  AP+E+EF + LP 
Sbjct: 499 AAVIGKPDPLLGETVKVFVSLKSGFTASQALHDELLGHGRKRLGAVVAPKELEFVEALPH 558

Query: 545 TRSGKIMRRVLKAWELNLPAGDLSTMED 572
           TRSGK+MRR+LKA EL LP GD S++E+
Sbjct: 559 TRSGKLMRRLLKARELGLPEGDTSSLEN 586


Lambda     K      H
   0.318    0.136    0.425 

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: 987
Number of extensions: 49
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 572
Length of database: 588
Length adjustment: 36
Effective length of query: 536
Effective length of database: 552
Effective search space:   295872
Effective search space used:   295872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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