GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_19945
          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:

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