GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_19945
          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:

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