GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gnl in Pseudomonas stutzeri RCH2

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate GFF4068 Psest_4141 3-carboxymuconate cyclase

Query= uniprot:Q9HWH7
         (388 letters)



>lcl|FitnessBrowser__psRCH2:GFF4068 Psest_4141 3-carboxymuconate
           cyclase
          Length = 397

 Score =  338 bits (866), Expect = 2e-97
 Identities = 194/391 (49%), Positives = 254/391 (64%), Gaps = 14/391 (3%)

Query: 5   PTLCLLALAPLTGV----APQAQAASLYNLLVGTYTEGS-SEGIQVYRFDGADGSVKG-P 58
           PTL  L  A L G       +A+   ++ +L+G+YT  S S GI   RFD A G +   P
Sbjct: 10  PTLLRLVFALLVGALLAGGARAETDDMH-ILIGSYTHDSDSPGILRLRFDPATGQIDPKP 68

Query: 59  LRVAHTSNPSYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTL 118
           ++   + NPS+L     +  L+  NENG     D VGR ++++ D  S   Q I Q  +L
Sbjct: 69  VQTLTSDNPSWLVLDDKRGRLYATNENGPA-HADPVGRVSAWQLDS-SSEHQLIGQNISL 126

Query: 119 ADHPTYSSLSHDGRYLFVANYSVQPE--GSVAVLPVRADGSLAPVVQVESHQASKVHP-R 175
            D PT++SLSHDGRYLF++NY  +P   GS+AV+P+  DG   PV Q+ +HQ+S VHP R
Sbjct: 127 GDEPTHASLSHDGRYLFISNYGSRPNPGGSLAVMPLAEDGHPLPVTQILAHQSSGVHPER 186

Query: 176 QVSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPRH 235
           Q S HVHS V SPDG+ L   DLGAD+VFVYRY P+ AERPLQA +PA +  PPGSGPRH
Sbjct: 187 QRSAHVHSAVPSPDGKRLLVSDLGADRVFVYRYDPQNAERPLQADEPASIELPPGSGPRH 246

Query: 236 LIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGR 295
           L+F  +G+ AYL LELS QV  F +  NG L + Q  DL  AG   +   GA+H SADGR
Sbjct: 247 LVFHPNGKHAYLALELSAQVASFDYT-NGTLTRRQLLDLKDAGNDVRHSPGAIHSSADGR 305

Query: 296 FLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQL 355
           FL V +RGD N ++ FA++ A G LR ++RRS EG EPREFA +  GRF+L+ANQ SD+L
Sbjct: 306 FLYVSDRGDYNHIIVFAIE-ADGTLREIQRRSSEGREPREFAITADGRFMLIANQLSDEL 364

Query: 356 RVFARDPQSGQVGKTLQSVEVGSPSDLRFVA 386
            V  RDP SGQ+G+ LQ++ VG PSD++ +A
Sbjct: 365 VVIRRDPDSGQLGEKLQTLTVGRPSDIKLLA 395


Lambda     K      H
   0.318    0.135    0.395 

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: 590
Number of extensions: 47
Number of successful extensions: 15
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: 388
Length of database: 397
Length adjustment: 31
Effective length of query: 357
Effective length of database: 366
Effective search space:   130662
Effective search space used:   130662
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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