GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF4068
          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:

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