GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Kocuria flava HO-9041

Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate WP_058857241.1 AS188_RS00800 acetyl-CoA C-acetyltransferase

Query= SwissProt::P09110
         (424 letters)



>NCBI__GCF_001482365.1:WP_058857241.1
          Length = 396

 Score =  228 bits (580), Expect = 3e-64
 Identities = 159/395 (40%), Positives = 214/395 (54%), Gaps = 17/395 (4%)

Query: 33  ASAADVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVL 92
           +S  DVVV+ G RT   +   G     T  EL +  +   L+   + PEQ+  + +G+VL
Sbjct: 2   SSPTDVVVLSGARTPQGKI-LGQLASFTAAELGAHAVRHALERAGVAPEQVDYVLMGHVL 60

Query: 93  QPGAGAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVES 152
           Q GAG   AR A   + IP  VP  TVN+ C SGL AV   A  IR G  ++ +A G ES
Sbjct: 61  QAGAGQNPARQAAVTAGIPLDVPAETVNKVCLSGLVAVTHAARMIRAGEAEVVVAGGQES 120

Query: 153 MSLADRGNPG-----NITSRLMEKEKARDCLIP------MGITSENVAERFGISREKQDT 201
           M+ A     G     +     +E   A+D L+       MG  +E+      ISR +QD 
Sbjct: 121 MTSAPHLALGVRQGKSYGDLKLEDAVAKDGLVDVAACVSMGSLTESGNGERAISRAEQDE 180

Query: 202 FALASQQKAARAQSKGCFQAEIVPVTTTVHDDKGTKRSITVTQDEGIRPSTTMEGLAKLK 261
            A  S ++AARA  +G F+ EI PVT  V   KG    + V  D+G+RP  T E +A+L+
Sbjct: 181 VAAQSHRRAARAAEEGVFREEIAPVT--VPQRKGDP--LVVDTDQGVRPEATAESMARLR 236

Query: 262 PAFKKDGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGP 321
           PAF +DG+ TAGNSS +SDGAAA++L+ R  A+  GL  L V+ +   V  P   +   P
Sbjct: 237 PAFAQDGTITAGNSSPLSDGAAALVLSTREYAQRHGLEWLAVVGAPGQVAGPDTSLHSQP 296

Query: 322 AYAIPVALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGC 381
           + AI  A+ KAG +V D+D  EINEAFAS     +  L  P E+ N  GGAVA+GHP+G 
Sbjct: 297 SRAIEAAVAKAGWSVQDLDFIEINEAFASVLIQSLRDLDYPLERANVHGGAVAVGHPIGA 356

Query: 382 TGARQVITLLNELKRRGKRAYGVVSMCIGTGMGAA 416
           +GAR  +    EL RRG      VS+C G G G A
Sbjct: 357 SGARLALHAAFELARRG-TGRAAVSLCGGGGQGEA 390


Lambda     K      H
   0.317    0.134    0.385 

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: 441
Number of extensions: 27
Number of successful extensions: 3
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: 424
Length of database: 396
Length adjustment: 31
Effective length of query: 393
Effective length of database: 365
Effective search space:   143445
Effective search space used:   143445
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: 50 (23.9 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