GapMind for catabolism of small carbon sources

 

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

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate AO353_19945 AO353_19945 acetyl-CoA synthetase

Query= SwissProt::Q8GQN9
         (527 letters)



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

 Score =  187 bits (476), Expect = 7e-52
 Identities = 151/493 (30%), Positives = 233/493 (47%), Gaps = 19/493 (3%)

Query: 51  TYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLT 110
           +Y  L+L  NR  + L+T LG+ P +R+ V    G++     LG +K G V   +     
Sbjct: 81  SYARLSLLSNRFANVLKT-LGVVPGERLFVLCGRGLELYLGVLGGLKLGCVVSPLFCAFG 139

Query: 111 ESDYEYMLTDSAARVAVVSQELLP-LFAPMLGKVPTLEHLVV---AGG-----AGEDSLA 161
               E  L      V + S+ L     A +  ++P L+H+++    GG      G  SL 
Sbjct: 140 PEPIETRLRLGEGSVLLTSETLYRHKVAAIRERLPALKHVLLYDEEGGNTTPVEGTLSLH 199

Query: 162 ALLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREG 221
            LLA  ++ FE A T  D      ++SG+TG PKG +H+H  ++ T  +  +  L +   
Sbjct: 200 RLLANATDHFEIAHTTADSPALLHFTSGTTGTPKGVLHVHGAVL-THRVTGKYALDLHPD 258

Query: 222 DVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPT-L 280
           D+ + +A   +  G   G+I PL +G T+V+          +  L + Q  ++Y  PT +
Sbjct: 259 DIYWCSADPGWVTGTSYGIIAPLLLGVTSVVEGREFDAERWYRTLEKQQVTVWYTAPTAI 318

Query: 281 YASMLANPDCPKEGELR-LRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLS 339
              M A  +         LR   S GE L  +     Q   G+ I D    TE   I ++
Sbjct: 319 RLLMKAGAELAHSHRFPCLRFIASVGEPLNPEAVWWGQEVLGLPIHDNWWQTETGGIMIA 378

Query: 340 NR-AGDVHYGTSGKPVPGYRLRLIDEDGA-EITTAG--VAGELQISGPSSAVM--YWNNP 393
           N  A  +  G+ GKP+PG    ++    A E+   G    GEL +  P  A+   Y    
Sbjct: 379 NTVAMTIKPGSMGKPLPGVEAAVVVRGAAGELDYLGDNEVGELALKQPWPAMFRTYLGQE 438

Query: 394 EKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLE 453
           E+    F+  W  SGD    + +GYY + GRSDD++K +G  + P EVES+L+ H AV E
Sbjct: 439 ERYRQCFVAGWYLSGDLVRRDADGYYWFIGRSDDVIKSAGHLIGPFEVESSLMEHPAVAE 498

Query: 454 AAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPK 513
           AAV+G  D       K F+ LK G+ A +AL  +L  H +  L     P+ +EFV+ LP 
Sbjct: 499 AAVIGKPDPLLGETVKVFVSLKSGFTASQALHDELLGHGRKRLGAVVAPKELEFVEALPH 558

Query: 514 TATGKIQRFKLRS 526
           T +GK+ R  L++
Sbjct: 559 TRSGKLMRRLLKA 571


Lambda     K      H
   0.319    0.138    0.412 

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: 835
Number of extensions: 58
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: 527
Length of database: 588
Length adjustment: 36
Effective length of query: 491
Effective length of database: 552
Effective search space:   271032
Effective search space used:   271032
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 (21.7 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