GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Nocardioides daejeonensis MJ31

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_110205408.1 DNK54_RS02835 acetyl-CoA C-acetyltransferase

Query= reanno::Marino:GFF2751
         (415 letters)



>NCBI__GCF_003194585.1:WP_110205408.1
          Length = 386

 Score =  289 bits (739), Expect = 1e-82
 Identities = 176/407 (43%), Positives = 242/407 (59%), Gaps = 23/407 (5%)

Query: 7   LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66
           + +AYIVDA+RTP+G+ GGAL+A+ + DLGA  + AL +R   +D + +DDV+ GC +  
Sbjct: 1   MAEAYIVDAVRTPVGKRGGALAAMHSADLGAHSLAALMQR-TGVDPAAVDDVIMGCCDTI 59

Query: 67  GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126
           G    DVAR + L+AGLP  VPG TI+R CGS   +V  AA+ + +G   L++AGG+++M
Sbjct: 60  GSQAGDVARTAWLVAGLPDHVPGVTIDRQCGSSQQSVHFAAQGVMSGTQDLVVAGGLQNM 119

Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPE--TAENVAADFGISR 184
           S  P       +     +  F  + GW         +YG   + +  +AE +A  + +SR
Sbjct: 120 SAIPISSAMLVAQQYGFSTPFAESPGW-------VARYGDVEVSQFNSAEMIAEKWDLSR 172

Query: 185 EDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKLASLP 244
           E+ + FAL S  R   A  EGR  AEI PV I     D  + DTD+ PR+TSLEK+A L 
Sbjct: 173 EEMERFALESHTRAKQAIAEGRFKAEIAPVEI-----DGTLFDTDQCPRDTSLEKMAGLD 227

Query: 245 TPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGP 304
            P +  G +TAG AS + DG+ ALL+A   A+K + L PRAR+  ++  G +P  M  GP
Sbjct: 228 -PLQPGGRITAGVASQICDGSAALLIASEQAVKDHGLTPRARIHHISVRGDDPIWMLTGP 286

Query: 305 APATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPL 364
             AT+  L   G+ + D+D+ E NEAFA+  LA  ++ G P D   VN NGG IALGHP+
Sbjct: 287 IRATQYALEKTGMSIDDIDLFECNEAFASVVLAWMKETGAPHD--KVNVNGGGIALGHPI 344

Query: 365 GMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411
           G +GARL+TT LNELER        RY L TMC G GQ    IIER+
Sbjct: 345 GATGARLMTTLLNELER-----TGGRYGLQTMCEGGGQANVTIIERL 386


Lambda     K      H
   0.318    0.133    0.382 

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: 428
Number of extensions: 19
Number of successful extensions: 7
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: 415
Length of database: 386
Length adjustment: 31
Effective length of query: 384
Effective length of database: 355
Effective search space:   136320
Effective search space used:   136320
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