GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Novosphingobium fuchskuhlense FNE08-7

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_067913759.1 AQZ52_RS17075 acetyl-CoA C-acyltransferase

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



>NCBI__GCF_001519075.1:WP_067913759.1
          Length = 416

 Score =  248 bits (633), Expect = 2e-70
 Identities = 173/436 (39%), Positives = 231/436 (52%), Gaps = 55/436 (12%)

Query: 1   MNEALIIDAVRTPIG---RYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCA 57
           M EA IIDAVRTP G      GAL+ +    L A  +KA+  R+  LD   VDD+I+  +
Sbjct: 1   MAEAYIIDAVRTPRGVGKPGKGALSHLHPQHLAATVMKAIAERN-NLDTGTVDDIIWSTS 59

Query: 58  NQAGEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGV 117
           +Q G+   ++ RMAAL AG  ++  GTTL+R CG G+ +V  AA  +  G    ++AGG 
Sbjct: 60  SQVGKQGGDLGRMAALAAGYNITASGTTLDRFCGGGITSVNLAAATVMSGMEDCVIAGGT 119

Query: 118 ESMSRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQG-FGIDSM-PETAENVAAQF- 174
           E MS            F  +    +   G  F  +LM  G   +D++ P++ + +     
Sbjct: 120 EMMS------------FTAANAAAEANAG--FPPRLMGSGNAALDALHPQSHQGICGDAI 165

Query: 175 ----NISRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDT 230
                ISR   DA AL SQ +A  AI  GR  K +V V     +     ++H+E PR +T
Sbjct: 166 ATIEGISREALDALALVSQQRADVAIKEGRFNKSVVPV---LNEDGTVALDHEEFPRPET 222

Query: 231 TLEQLAKLGTPFRQ------GGSVT-------------------AGNASGVNDGACALLL 265
           T E LA L   F        GG +T                   AGN+SGV DGA ALL+
Sbjct: 223 TAEGLASLKPAFAAMMDFDLGGGMTFRKQINRRYPDVDIKPVHHAGNSSGVVDGAAALLI 282

Query: 266 ASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPVPATRKVLELTGLALADMDVIELNEA 325
            S   A++HGLK RAR+V  A  G +P +M   PVPA +KVL   GL   D+DV E+NEA
Sbjct: 283 TSPTYAEKHGLKPRARIVAYANQGDDPTLMLNAPVPAAKKVLAKAGLTKEDIDVWEINEA 342

Query: 326 FAAQGLAVLRELGLADDDERVNPNGGAIALGHPLGMSGARLVTTALHELEERQGRYALCT 385
           FA      +R+L L  D  +VN NGGA+ALGHP+G +G+ L+ TAL ELE   GRY L T
Sbjct: 343 FAVVAEKFIRDLDL--DRAKVNINGGAMALGHPIGATGSILIGTALDELERSGGRYGLVT 400

Query: 386 MCIGVGQGIALIIERI 401
           MC   G   A+IIER+
Sbjct: 401 MCAAGGMAPAIIIERL 416


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: 463
Number of extensions: 31
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: 401
Length of database: 416
Length adjustment: 31
Effective length of query: 370
Effective length of database: 385
Effective search space:   142450
Effective search space used:   142450
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 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