GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Herbaspirillum seropedicae SmR1

Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate HSERO_RS19370 HSERO_RS19370 gluconolactonase

Query= BRENDA::Q64374
         (299 letters)



>FitnessBrowser__HerbieS:HSERO_RS19370
          Length = 302

 Score =  162 bits (411), Expect = 7e-45
 Identities = 97/302 (32%), Positives = 156/302 (51%), Gaps = 14/302 (4%)

Query: 2   SSIKVECVLRENYRCGESPVWEEASQSLLFVDIPSKIICRWDTVSNQVQRVAVDAPVSSV 61
           S+  V     E    GESP+W     +L ++DIP K + R    S Q +R  +     S+
Sbjct: 7   SAAAVTVAFPEPMLLGESPLWHAQEAALYWIDIPGKAVHRLHPESGQHKRWDLPEEPGSI 66

Query: 62  ALRQLGGYVATIGTKFCALNWENQSVFVLAMVDEDKKNNRFNDGKVDPAGRYFAGTMAEE 121
                GG V  I T    LN +  ++ +L     D    RFNDG+ D +GR++ GT+ E 
Sbjct: 67  VRHAQGGLVVAIRTGMFHLNTDTGALTLLLAAPYDSSRIRFNDGRCDASGRFWCGTIYEP 126

Query: 122 TAPAVLERHQGSLYSLFPDHSVKKYFDQVDISNGLDWSLDHKIFYYIDSLSYTVDAFDYD 181
                 +R  G+LY  F  ++++     V  SNGL +S D ++ Y+ ++ ++ ++ +DYD
Sbjct: 127 R-----DRDGGTLY-CFERNALRDAHHAVVTSNGLAFSSDQRLMYHANTPAHRINLYDYD 180

Query: 182 LQTGQISNRRIVYKMEKDEQI------PDGMCIDAEGKLWVACYNGGRVIRLDPETGKRL 235
           L TG  SN R++ + + D+        PDG  +D++G  W A + GGRV+RL P+ G+ L
Sbjct: 181 LATGATSNCRLLRQFDSDKSAPDYGGRPDGAAVDSQGAYWCAMFEGGRVLRLSPQ-GEIL 239

Query: 236 QTVKLPVDKTTSCCFGGKDYSEMYVTCARDGLNAEGLLRQPDAGNIFKITGLGVKGIAPY 295
           Q ++LP    T   FGG D   +Y+T  R+G +   L + P++G +  +  + V G   Y
Sbjct: 240 QEIRLPARCPTMVAFGGDDLRTLYITTGRNGRSPAELAQYPESGCVLAVR-VDVPGQLEY 298

Query: 296 SY 297
           SY
Sbjct: 299 SY 300


Lambda     K      H
   0.319    0.137    0.419 

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: 256
Number of extensions: 14
Number of successful extensions: 4
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: 299
Length of database: 302
Length adjustment: 27
Effective length of query: 272
Effective length of database: 275
Effective search space:    74800
Effective search space used:    74800
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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