GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Shewanella loihica PV-4

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 5209735 Shew_2188 long-chain-fatty-acid--CoA ligase (RefSeq)

Query= BRENDA::A7KUK6
         (562 letters)



>FitnessBrowser__PV4:5209735
          Length = 557

 Score =  210 bits (534), Expect = 1e-58
 Identities = 169/570 (29%), Positives = 265/570 (46%), Gaps = 52/570 (9%)

Query: 9   LVDIPEVDLWTFLFERKDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWR 68
           ++D  +      LFE     Y D         T    TY+ L + S  F   L+   + +
Sbjct: 16  IIDAKQYSSLIDLFESSVAKYADQPAFVNMGAT---LTYRKLEERSRAFAAYLQNELKLQ 72

Query: 69  KGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVL 128
           KGD +A+  PN +  P+ ++G L AG  +   NP YT  EL  QL +S AK +V  ++  
Sbjct: 73  KGDRVAIMMPNLLQYPIALFGILRAGMVVVNVNPLYTPRELKHQLNDSGAKAIVVVSNFA 132

Query: 129 PVAREAAKKVGMPEDRIILIGD------------------QRDPDARVKHFTSVRNISGA 170
               +  ++  +    +  +GD                  +  P   + H  S+R     
Sbjct: 133 NTLEQVVEQTPVKSVILTGLGDLLSAPKRTLVNFVVKYIKKMVPKYHLPHAISMRQSLSK 192

Query: 171 TRYRKQKITPA---KDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGG 227
            R R Q + P     D+AFL Y+ GTTGV KG M++H NIV+N+ Q   A   +L+    
Sbjct: 193 GR-RLQYVKPTIKGDDIAFLQYTGGTTGVSKGAMLTHGNIVSNLLQADAAYSPLLA---- 247

Query: 228 PDGKGDRVLAFLPFYHIYGLTCLITQALYKGYH-LIVMSKFDIEKWCAHVQNYRCSFSYI 286
            DGK + V+  LP YHI+ LT      L+KG + L++ +  DI  + + ++ +  +    
Sbjct: 248 -DGK-EFVVTALPLYHIFALTVNCLLFLHKGANNLLITNPRDIPAFVSELKKHPFTALTG 305

Query: 287 VPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSP- 345
           V  +   L         D S+L++   G   + + + +      K  + +GYGL+E SP 
Sbjct: 306 VNTLFNALVSSEEFKTLDFSNLKLSIGGGMAVQRAVADKWQGITKTRLLEGYGLTEASPL 365

Query: 346 -TTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLG 404
            T      E +    GS+G   P          E+G+    + +GE GEL+ KGP V  G
Sbjct: 366 LTCCPYNLEGYN---GSIG--FPVANTDMQVRDEEGNV---LPQGETGELFAKGPQVMKG 417

Query: 405 YHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVD 464
           Y + PE T   + +DG+  TGD+GY D +G F+I DR K++I   GF V P E+E  +  
Sbjct: 418 YWQRPEETAKVIDKDGYLATGDIGYMDEQGFFFIVDRKKDMILVSGFNVFPNEVEEVVAL 477

Query: 465 NDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRL 524
           +  + +VA +G+  E  G E+    VV   KS +          ++IK     +  +K +
Sbjct: 478 HPKVLEVAAVGVPHEVSG-ELVKVFVVPKDKSLTE--------EQVIKHCRHHLTGYK-I 527

Query: 525 RGGVHFVDEIPKNPSGKILRRILKQKFKGA 554
              V F DE+PK+  GKILRR L+ + K A
Sbjct: 528 PKLVEFRDELPKSNVGKILRRELRDEAKSA 557


Lambda     K      H
   0.317    0.136    0.410 

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: 685
Number of extensions: 33
Number of successful extensions: 6
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: 562
Length of database: 557
Length adjustment: 36
Effective length of query: 526
Effective length of database: 521
Effective search space:   274046
Effective search space used:   274046
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.

Links

Downloads

Related tools

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