GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Escherichia coli BW25113

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 15923 b1805 acyl-CoA synthase (NCBI)

Query= BRENDA::D3GE78
         (556 letters)



>FitnessBrowser__Keio:15923
          Length = 561

 Score =  191 bits (484), Expect = 8e-53
 Identities = 163/523 (31%), Positives = 251/523 (47%), Gaps = 38/523 (7%)

Query: 46  LTTHDLRLWSQRLAAGLRKS-GLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTF 104
           +T   L   S+  AA L++  GL++GDRV L   N L +PV   G++ AG I    NP +
Sbjct: 49  MTFRKLEERSRAFAAYLQQGLGLKKGDRVALMMPNLLQYPVALFGILRAGMIVVNVNPLY 108

Query: 105 VARELAYQLQDSGATYLLCASNSLETGLEAAKQAKLPQSHIFAYDTSIYDGVTNPQKGCA 164
             REL +QL DSGA+ ++  SN   T LE        Q  I    T + D ++   KG  
Sbjct: 109 TPRELEHQLNDSGASAIVIVSNFAHT-LEKVVDKTAVQHVIL---TRMGDQLSTA-KGTV 163

Query: 165 ------YWSDLLASEEEGAAFTWD---------ELSTPALSSTTLA-LNYSSGTTGRPKG 208
                 Y   L+       A ++          +   P L    LA L Y+ GTTG  KG
Sbjct: 164 VNFVVKYIKRLVPKYHLPDAISFRSALHNGYRMQYVKPELVPEDLAFLQYTGGTTGVAKG 223

Query: 209 VEISHRNYVANMLQYCHTAS--LHPDYKARLERSRWLCFLPMYHAMAQNIFIAAAL-YRA 265
             ++HRN +AN+ Q   T    LHP       +   +  LP+YH  A  I     +    
Sbjct: 224 AMLTHRNMLANLEQVNATYGPLLHPG------KELVVTALPLYHIFALTINCLLFIELGG 277

Query: 266 TPVYIMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPL 325
             + I +  D   +++   ++  T    V  +  AL  +    Q D SS+ L   G  P+
Sbjct: 278 QNLLITNPRDIPGLVKELAKYPFTAITGVNTLFNALLNNKEFQQLDFSSLHLSAGGGMPV 337

Query: 326 GREVCEEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEIST-SASVGELNANCEAKIMF 384
            + V E   KL   G+  + +G+G+TE    V+  NP +I   S S+G    + EAK++ 
Sbjct: 338 QQVVAERWVKL--TGQY-LLEGYGLTECAPLVSV-NPYDIDYHSGSIGLPVPSTEAKLVD 393

Query: 385 DGVEVKERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVD 444
           D          GEL V+ P VM GYW+   AT E   ++GWL TGDIA +D++G   +VD
Sbjct: 394 DDDNEVPPGQPGELCVKGPQVMLGYWQRPDATDEI-IKNGWLHTGDIAVMDEEGFLRIVD 452

Query: 445 RMKELIKVKGNQVAPAELEALLLEHPAISDVAVIGVVINNDERPRAYVVLRPGQSATANE 504
           R K++I V G  V P E+E ++++HP + +VA +GV   +        V++   S T   
Sbjct: 453 RKKDMILVSGFNVYPNEIEDVVMQHPGVQEVAAVGVPSGSSGEAVKIFVVKKDPSLTEES 512

Query: 505 IAHYLDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQAK 547
           +  +   +++ +K +   V F + +PK+  GKILR +LR++A+
Sbjct: 513 LVTFCRRQLTGYK-VPKLVEFRDELPKSNVGKILRRELRDEAR 554


Lambda     K      H
   0.319    0.134    0.403 

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: 662
Number of extensions: 35
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: 2
Length of query: 556
Length of database: 561
Length adjustment: 36
Effective length of query: 520
Effective length of database: 525
Effective search space:   273000
Effective search space used:   273000
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