Aligments for a candidate for paaK in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for paaK in Shewanella oneidensis MR-1

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 201721 SO2581 long-chain-fatty-acid--CoA ligase (NCBI ptt file)

Query= BRENDA::A7KUK6
         (562 letters)



>lcl|FitnessBrowser__MR1:201721 SO2581 long-chain-fatty-acid--CoA
           ligase (NCBI ptt file)
          Length = 557

 Score =  207 bits (528), Expect = 7e-58
 Identities = 166/533 (31%), Positives = 252/533 (47%), Gaps = 49/533 (9%)

Query: 46  TYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYT 105
           TY+ L + S  F   L+   + +KGD +AL  PN +  P+ ++G L AG  +   NP YT
Sbjct: 50  TYRKLEERSRAFAAYLQNELKLQKGDRVALMMPNLLQYPIALFGILRAGMVVVNVNPLYT 109

Query: 106 VDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGDQRDPDAR-------- 157
             EL  QL +S AK +V  ++      E   +  +    I  +GD      R        
Sbjct: 110 PRELKHQLIDSGAKAIVVVSNFARTLEEVVDQTPVKSVIITGLGDLLSAPKRTLVNFVVK 169

Query: 158 ----------VKHFTSVRNISGATRYRKQKITPA---KDVAFLVYSSGTTGVPKGVMISH 204
                     + H  S+R      R R Q + P     D+AFL Y+ GTTGV KG M++H
Sbjct: 170 YIKKLVPKYDLPHALSMRETLSRGR-RMQYVKPVITGDDLAFLQYTGGTTGVSKGAMLTH 228

Query: 205 RNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKG-YHLIV 263
            N+VAN+ Q   A    L      DG  + V+  LP YHI+ LT      L+KG  +L++
Sbjct: 229 SNVVANVLQANGAYSPALR-----DGS-EFVVTALPLYHIFALTVNCLLFLHKGSQNLLI 282

Query: 264 MSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELV 323
            +  DI  + A ++ Y  +    V  +   L       + D S L++   G   + + + 
Sbjct: 283 TNPRDIPGFVAELKKYPFTALTGVNTLFNALVNSSDFSELDFSRLKLSIGGGMAVQKAVA 342

Query: 324 EAVYSRIKVGIKQGYGLSETSP--TTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGS 381
           +   +  K  + +GYGL+E SP  T      + +    GS+G   P+     + + +D  
Sbjct: 343 DKWQNITKTRLLEGYGLTEASPLLTCCPYNLDGYN---GSIGFPAPST---LIQVRDDAG 396

Query: 382 EPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDR 441
               + +GE GEL+ KGP +  GY + PE T   +  DGW  TGD+GY D +G FYI DR
Sbjct: 397 NV--LPQGETGELFGKGPQIMKGYWQRPEETAKVIDNDGWLATGDIGYMDEQGFFYIVDR 454

Query: 442 VKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGT 501
            K++I   GF V P E+E  +  +  + +VA +G+ ++  G E+    VV+  KS +   
Sbjct: 455 KKDMILVSGFNVFPNEVEEVVALHPKVIEVAAVGVPNDASG-ELVKVFVVKKDKSLT--- 510

Query: 502 SEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILKQKFKGA 554
                A  IIK     +  +K +   V F DE+PK   GKILRR L+ + K A
Sbjct: 511 -----AEDIIKHCRVHLTGYK-VPKLVEFRDELPKTNVGKILRRELRDEVKRA 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: 695
Number of extensions: 38
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.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 preprint 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

GapMind for catabolism of small carbon sources