GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Escherichia coli BW25113

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate 16332 b2224 acetyl-CoA acetyltransferase (NCBI)

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__Keio:16332
          Length = 394

 Score =  325 bits (833), Expect = 1e-93
 Identities = 193/403 (47%), Positives = 259/403 (64%), Gaps = 12/403 (2%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M   +I+ AVRT IG + G+LAS  A DLGA  +KA I R  ++D   VD+VI G   QA
Sbjct: 1   MKNCVIVSAVRTAIGSFNGSLASTSAIDLGATVIKAAIER-AKIDSQHVDEVIMGNVLQA 59

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           G   +N AR A L +GL  +V G T+N++CGSGL +V  AA+A++ G+A  ++AGG+E+M
Sbjct: 60  GL-GQNPARQALLKSGLAETVCGFTVNKVCGSGLKSVALAAQAIQAGQAQSIVAGGMENM 118

Query: 121 SRAPFVMGKSEQAFGR--SAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178
           S AP+++    ++  R    +++D  +     + LM    G   M  TAENVA ++ I+R
Sbjct: 119 SLAPYLLDAKARSGYRLGDGQVYDVILR----DGLMCATHGYH-MGITAENVAKEYGITR 173

Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKL 238
             QD  AL SQ KAAAAI +G    EIV V +  RK    +   DE P+ ++T E L  L
Sbjct: 174 EMQDELALHSQRKAAAAIESGAFTAEIVPVNVVTRK-KTFVFSQDEFPKANSTAEALGAL 232

Query: 239 GTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIG 298
              F + G+VTAGNASG+NDGA AL++    AA   GL   AR+   A+ GV P +MG+G
Sbjct: 233 RPAFDKAGTVTAGNASGINDGAAALVIMEESAALAAGLTPLARIKSYASGGVPPALMGMG 292

Query: 299 PVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHP 358
           PVPAT+K L+L GL LAD+D+IE NEAFAAQ LAV + LG   D E+VN NGGAIALGHP
Sbjct: 293 PVPATQKALQLAGLQLADIDLIEANEAFAAQFLAVGKNLGF--DSEKVNVNGGAIALGHP 350

Query: 359 LGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           +G SGAR++ T LH ++ R     L T+CIG GQGIA++IER+
Sbjct: 351 IGASGARILVTLLHAMQARDKTLGLATLCIGGGQGIAMVIERL 393


Lambda     K      H
   0.319    0.134    0.384 

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: 411
Number of extensions: 16
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: 401
Length of database: 394
Length adjustment: 31
Effective length of query: 370
Effective length of database: 363
Effective search space:   134310
Effective search space used:   134310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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