GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Novosphingobium barchaimii LL02

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_013054067.1 V474_RS21625 acetyl-CoA C-acetyltransferase

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



>NCBI__GCF_001046635.1:WP_013054067.1
          Length = 403

 Score =  288 bits (737), Expect = 2e-82
 Identities = 173/404 (42%), Positives = 245/404 (60%), Gaps = 8/404 (1%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           +  A I+  +RT +G++ G L+++ A  LGA  +KAL+ R   +D   VDDV++G    +
Sbjct: 3   LRRAAIVSPLRTAVGKFGGGLSALTAGQLGATIIKALVERSG-IDPERVDDVVFGHGYPS 61

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GE   ++ R + L AG+P +VPG  L+R CGSGL A+  AA  ++ G A +++AGG ESM
Sbjct: 62  GEAP-SIGRWSWLAAGMPQNVPGFQLDRRCGSGLQAIIEAAMMVQTGAADVVVAGGAESM 120

Query: 121 SRAP-FVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRA 179
           S    +     + A   S E+ D     R +++ +++   I  M ETAEN+A  + I+R 
Sbjct: 121 SNVEHYSTALRKGARMGSLELHDRLTRARLMSQPIERYGVITGMIETAENLARDYGITRE 180

Query: 180 DQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLG 239
             DA+A+RS  +AAAA   G+ A EIV V + Q++G   I + DE  R D +LE L  L 
Sbjct: 181 QSDAYAVRSHQRAAAAWREGKFADEIVPVAVPQKRGEPVIFDRDEGFREDASLETLGGL- 239

Query: 240 TPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGP 299
            P  +GG VTAGNAS  ND A A L+ + +   + GL+     VG A AG +P  MGIGP
Sbjct: 240 KPI-EGGVVTAGNASQQNDAAAACLVVAEDQLAKLGLEPSGWFVGWAAAGCDPSRMGIGP 298

Query: 300 VPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDER---VNPNGGAIALG 356
           V A +++   TGL   DMD+IE+NEAFAAQ LA+L+     +DD R   +N NG  I+LG
Sbjct: 299 VGAVQRLFARTGLGWDDMDLIEINEAFAAQVLALLKAWEWGEDDSRLDKLNVNGSGISLG 358

Query: 357 HPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400
           HP+G++GAR+  T L+E+  R  RY L TMCIG GQG+A I ER
Sbjct: 359 HPIGVTGARIAATMLNEMRRRDARYGLETMCIGGGQGLAAIFER 402


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: 459
Number of extensions: 33
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: 401
Length of database: 403
Length adjustment: 31
Effective length of query: 370
Effective length of database: 372
Effective search space:   137640
Effective search space used:   137640
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