GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Pontibacillus litoralis JSM 072002

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_036834463.1 N784_RS09620 acetyl-CoA C-acetyltransferase

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



>NCBI__GCF_000775615.1:WP_036834463.1
          Length = 395

 Score =  273 bits (698), Expect = 7e-78
 Identities = 167/399 (41%), Positives = 234/399 (58%), Gaps = 14/399 (3%)

Query: 12  IVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAGEDNR 71
           IV  +RTP G+ GG+LSA+ A  LG + IKA  ER  D +  K+D+V+ G   Q G+  +
Sbjct: 6   IVSGVRTPFGKLGGSLSALSAAQLGGVAIKAALER-ADFEPEKVDEVIMGTVLQGGQ-GQ 63

Query: 72  DVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMSRAPF 131
             +R +   AG+P +V   TIN++C SGM +V  A + IR G+ Q+++AGG+ESMS AP+
Sbjct: 64  IPSRQASRNAGIPWEVKTETINKVCASGMRSVTLADQLIRLGDEQVIVAGGMESMSNAPY 123

Query: 132 VMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISREDQDAFA 191
            M KA   F     + D  +    V+  L   +    M       A+++ +SRE+QD +A
Sbjct: 124 FMPKARFGF----RMGDQVVKDLMVHDGLTCTFKGVHMGTYGNETASEYELSREEQDEWA 179

Query: 192 LRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRET-SLEKLASLPTPFREN 250
            RS Q   AA + G  A EITPV +P+RK DPL+V+ DE PR+T S+E L  L   F  N
Sbjct: 180 YRSHQLAVAAMENGTFAEEITPVEVPQRKGDPLLVEKDEAPRKTTSVEALRKLNPVFDAN 239

Query: 251 GTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPAPATRK 310
           GT+TAGNA GVNDGA A+LL        +  +P A ++A     VE +     P      
Sbjct: 240 GTITAGNAPGVNDGAGAMLLMSQQYASAHGYQPMATILAHDEVAVEAKDFPKTPGLVMNS 299

Query: 311 VLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLGMSGAR 370
           +L  AG  L ++D+ E+NEAFAA +LA  +  GL  D + VN NGGAIALGHP+G SGAR
Sbjct: 300 LLKKAGKTLEEIDLFEVNEAFAAVSLASGKIAGL--DLDKVNVNGGAIALGHPIGASGAR 357

Query: 371 LVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIE 409
           ++ T ++EL+RR          +  +C G GQG A++IE
Sbjct: 358 IIITLMHELKRRGGG-----IGIAAICSGGGQGDAVMIE 391


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: 349
Number of extensions: 13
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: 415
Length of database: 395
Length adjustment: 31
Effective length of query: 384
Effective length of database: 364
Effective search space:   139776
Effective search space used:   139776
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.

Links

Downloads

Related tools

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