GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Pseudomonas fluorescens FW300-N1B4

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Pf1N1B4_3904 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= metacyc::MONOMER-20679
         (395 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904
          Length = 383

 Score =  244 bits (624), Expect = 2e-69
 Identities = 157/399 (39%), Positives = 221/399 (55%), Gaps = 25/399 (6%)

Query: 5   VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQQGAT 63
           VIV   RTP+G++  G    T    +  H I   ++R   +DP EVEDV+ G   Q    
Sbjct: 1   VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPSEVEDVIWGCVNQTLEQ 60

Query: 64  GGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLV 123
           G NIAR A L   +P T AG T+ R C S + A+  AA++++    ++ V GG E +  V
Sbjct: 61  GWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHV 120

Query: 124 QNDKMNTFHAVDP----ALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179
                +  H VDP    +L A K    M +  TAE + K +GI+RE+QD + + S +   
Sbjct: 121 -----SMMHGVDPNPHMSLYAAKASGMMGL--TAEMLGKMHGITREQQDAFGVRSHQLAH 173

Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLK-AVRG 238
            A   GKF DEI P+           G +   D     DE  RPETT E LA LK A   
Sbjct: 174 KATLEGKFKDEIIPMQGY-----DENGFLKLFDY----DETIRPETTLESLAALKPAFNP 224

Query: 239 EGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAV 298
           +G T+TAG +SQ++DGAS  ++MS + A   G++P+ + R M   G +P  MG GPV A 
Sbjct: 225 KGGTVTAGTSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPAT 284

Query: 299 PRLLKRHGLSVDDIGLWELNEAFAVQVL-YCRDKLGIDP--EKLNVNGGAISVGHPYGMS 355
            + LKR GL ++DI  +ELNEAFA Q L   +D   +D   EK+N++GGAI++GHP+G S
Sbjct: 285 QKALKRAGLGINDIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCS 344

Query: 356 GARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           GAR++G  L   ++    + V TMC+G G G + +FE V
Sbjct: 345 GARISGTLLNVMKQNGGTFGVATMCIGLGQGISTVFERV 383


Lambda     K      H
   0.316    0.134    0.378 

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: 386
Number of extensions: 22
Number of successful extensions: 5
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: 395
Length of database: 383
Length adjustment: 30
Effective length of query: 365
Effective length of database: 353
Effective search space:   128845
Effective search space used:   128845
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 (21.6 bits)
S2: 50 (23.9 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