GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Kocuria flava HO-9041

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_058857116.1 AS188_RS00055 long-chain fatty acid--CoA ligase

Query= BRENDA::A7KUK6
         (562 letters)



>NCBI__GCF_001482365.1:WP_058857116.1
          Length = 568

 Score =  168 bits (426), Expect = 5e-46
 Identities = 149/513 (29%), Positives = 233/513 (45%), Gaps = 62/513 (12%)

Query: 70  GDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLP 129
           GD +A+  PN     V  +  L  G  +   NP YT  EL  Q ++  A+       V  
Sbjct: 82  GDRVAIVLPNCPQHIVAFYAVLRLGAVVVEHNPLYTAPELRHQFEDHGAR-------VAI 134

Query: 130 VAREAAKKV-GMPED----RIILIGDQRDPDARVKHFTSVRNISGATRYRKQKIT----- 179
           V   AA ++  +PED     ++ +   +    R +   ++R    A R  + ++T     
Sbjct: 135 VWDRAADRIRSLPEDLRLDAVVAVDVTQAMPRRTR--AALRLPLPAARASRAQLTGPAPG 192

Query: 180 --------------------PAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEG 219
                                A D+A L Y+SGTTG+PKG M++HRN+ +N         
Sbjct: 193 TIPWRRLVAAEPLAADHPRPTAHDLALLQYTSGTTGLPKGAMLTHRNLESNA-------- 244

Query: 220 EMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNY 279
            ++  +    G+ + V   LP +H +GLT  +T A+  G  L++      +     ++  
Sbjct: 245 -LMGQHWLHSGEDEVVHGVLPLFHAFGLTLGVTFAMSLGARLVLFPTVRADLVLKALRRS 303

Query: 280 RCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYG 339
           R +    VPPV   L         DL  + +  SGA  L   LVE         + +GYG
Sbjct: 304 RPTVLPAVPPVYEKLLDAAEERGADLRGIAVAVSGAMTLPVPLVERWERATGGMLVEGYG 363

Query: 340 LSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGP 399
           L+E SP        D R A GS+G   P+ + + +    D    ++V  G  GEL+++GP
Sbjct: 364 LTECSPLVACNPLNDSRRA-GSIGVPFPSTEIRLV----DPETLEDVPRGHEGELWVRGP 418

Query: 400 NVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELE 459
            VF GY + PE T   L EDGW +TGDV   D  G   + DR+KE+I   GF V P E+E
Sbjct: 419 QVFRGYWKRPEETARVLVEDGWLRTGDVVTVDDDGFLRVVDRIKEVIITGGFNVAPTEVE 478

Query: 460 GYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVA 519
             L  +D + D AV+G++ +  G E  +A VV      + G    ++A R  +    KV 
Sbjct: 479 TALKLHDDVADAAVVGLD-DGRGGEAVVAAVV-----LAPGAVLDEQALR--EHCYGKVT 530

Query: 520 SHKRLRGGVHFVDEIPKNPSGKILRRILKQKFK 552
            +K  R  +  V+++P+   GK LRR ++ + +
Sbjct: 531 RYKVPR-RIVAVEDLPRTMLGKTLRREVRARLE 562


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: 647
Number of extensions: 31
Number of successful extensions: 6
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: 562
Length of database: 568
Length adjustment: 36
Effective length of query: 526
Effective length of database: 532
Effective search space:   279832
Effective search space used:   279832
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 24 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