GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Pseudarthrobacter sulfonivorans Ar51

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase

Query= BRENDA::Q1XGK8
         (486 letters)



>NCBI__GCF_001484605.1:WP_058929223.1
          Length = 508

 Score =  338 bits (867), Expect = 3e-97
 Identities = 186/480 (38%), Positives = 278/480 (57%), Gaps = 6/480 (1%)

Query: 8   INGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAAL-KGPWGKLSVAER 66
           I+GA+V S+SG TF  ++P +    G V  A   +VD AV+AAR A  +G W +   ++R
Sbjct: 25  IDGAWVQSSSGETFACVDPYDNASWGRVPAATVEDVDRAVRAARRAFDEGGWPQTLPSQR 84

Query: 67  AEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANEAF 126
           A +L R AD +T   DE    +  + GK     +   +  G     V A L + +     
Sbjct: 85  AALLRRFADLLTENADELARGQIHENGKLIGEMTWGALQMGQHAHYV-AGLAETIQGRTI 143

Query: 127 EMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPLT 186
           E   P+ A    +  R P GV+ +I+PWN PL+L++WK+  ALA GNTVV+KPSE TP +
Sbjct: 144 ESNWPNTAA---FTFREPIGVVAMITPWNSPLMLLSWKLFAALAAGNTVVIKPSEATPTS 200

Query: 187 ATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRAAAK 246
              + E+   AG P GV NVV GFG    G+ L +H  VD   FTG T  G  I + AA+
Sbjct: 201 TLRMAELAMEAGFPPGVINVVTGFG-QPTGSALVDHRGVDKIAFTGSTSAGRAINKQAAE 259

Query: 247 GVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDEFVA 306
              +V+LELGGK+  I+F+D D+D A+ G +   F   GQ C+G  RV V+  I+D+FV 
Sbjct: 260 RFARVTLELGGKSPNIIFSDADIDNAVHGAMAGIFGATGQTCMGGSRVLVQDSIYDDFVD 319

Query: 307 RLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDMPAHL 366
           R+    ++L +G P D + + GP+ +    +KV+ Y      +G  V+ GG      + L
Sbjct: 320 RMARATQALTLGDPLDPTVDMGPVSNRAQFQKVIDYVDLGQSEGAEVVAGGARCMTTSEL 379

Query: 367 AGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIWTEN 426
           + G + +PT++  +S++S +  EEIFGP   I  F  E+EA+++AN+  +GLA+ +WT +
Sbjct: 380 SKGLFFEPTVFANVSNESRLAQEEIFGPVASIIRFRDEDEAVKIANASDFGLAAGVWTND 439

Query: 427 GSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNICVKL 486
            SRAHR+  ++ +G VWVN++ L +    FGG KQSGIGRE G  +L+ YTE+K+  + L
Sbjct: 440 VSRAHRMIRRVRSGTVWVNTYRLTNYSVPFGGFKQSGIGRELGPDALDAYTEVKSAWIDL 499


Lambda     K      H
   0.318    0.136    0.411 

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: 662
Number of extensions: 29
Number of successful extensions: 5
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: 486
Length of database: 508
Length adjustment: 34
Effective length of query: 452
Effective length of database: 474
Effective search space:   214248
Effective search space used:   214248
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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