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

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 5210656 Shew_3084 AMP-dependent synthetase and ligase (RefSeq)

Query= BRENDA::A7KUK6
         (562 letters)



>FitnessBrowser__PV4:5210656
          Length = 531

 Score =  197 bits (502), Expect = 7e-55
 Identities = 149/487 (30%), Positives = 237/487 (48%), Gaps = 28/487 (5%)

Query: 70  GDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLP 129
           GD +A+  PN     +  +G L AG  +   NP YT  EL  Q ++S AK LV  + +LP
Sbjct: 66  GDKVAIQLPNITQFVIAAYGALRAGMILVNTNPLYTQRELIHQYRDSDAKALVVLSDLLP 125

Query: 130 ----VAREAAKKVGMPEDRIILIGDQRDPDARVKH--FTSVRNISGATRYRKQKITPAKD 183
               V  E   +  +    + LI  Q   D+++ H  F  V  +     YR  ++   + 
Sbjct: 126 TLETVIPETQIETVISTHPLDLIATQPQADSQLAHIGFNQVLALGSQAEYRPVEVAQ-QS 184

Query: 184 VAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRV-LAFLPFY 242
           +A L Y+ GTTG+ KG M+SH N++AN+ Q       + S       +G+ + +A LP Y
Sbjct: 185 LAALQYTGGTTGLSKGAMLSHSNLLANMLQ-------VQSRLASKFVEGEEIFIAPLPIY 237

Query: 243 HIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDK 302
           HIY            G  +++ +  DI      +  +  +    +  + + L        
Sbjct: 238 HIYAFMVNFVYFEQGGCSVLIPNPRDISALIQTMSQHPFTGFAGLNTLFVGLCHQQSFQA 297

Query: 303 YDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSV 362
            D S L++  SG   LTQ       S     I +GYGLSETSP           E +G++
Sbjct: 298 LDFSHLKITISGGTALTQAAASIWQSTTGCTISEGYGLSETSPVVSLNA--PGLECLGTI 355

Query: 363 GRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWF 422
           GR + + Q K +    D SE +EV +GE+GEL +KGP V  GY + PE T   ++ DG+F
Sbjct: 356 GRPVIDTQVKIL----DASE-QEVPQGEIGELAVKGPQVMSGYWQKPEETAKVMTSDGFF 410

Query: 423 QTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHG 482
           +TGD+      G   I DR K++I   GF V P E+E  L  ++++ + AVIG++    G
Sbjct: 411 KTGDIALATEDGMHKIVDRKKDMIIVSGFNVYPNEVEDVLAAHESVLECAVIGVDDSRSG 470

Query: 483 SEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKI 542
             V  A V+R  +  +  T +      +++   +++A++K L   + F+  +PK+  GKI
Sbjct: 471 EAVKAAIVLREPELANDATKQ-----ALLEHCRAQLAAYK-LPKIIEFMPALPKSTVGKI 524

Query: 543 LRRILKQ 549
           LRR L++
Sbjct: 525 LRRELRK 531


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: 631
Number of extensions: 25
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: 562
Length of database: 531
Length adjustment: 36
Effective length of query: 526
Effective length of database: 495
Effective search space:   260370
Effective search space used:   260370
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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