GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Novosphingobium fuchskuhlense FNE08-7

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_067910653.1 AQZ52_RS11395 aldehyde dehydrogenase family protein

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_001519075.1:WP_067910653.1
          Length = 481

 Score =  243 bits (621), Expect = 9e-69
 Identities = 156/471 (33%), Positives = 241/471 (51%), Gaps = 22/471 (4%)

Query: 35  KDYPLVINGE---RVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRY 91
           K  P  ING+      + A   ++NPA  EEV  RV+    +  ++A+ AA  AF+ +  
Sbjct: 5   KPLPSYINGQWALPATSTALFEAVNPAT-EEVCARVALCGPDDVDRAMAAARAAFDGYST 63

Query: 92  TSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIEL 151
           TS EER A++ +  A    R  E    +  E G P++ +    AE       + ++ +  
Sbjct: 64  TSLEERLALVEKLIAVFEARYDEMVTAISTEMGAPYDLSYNAQAEC---GPGHLKETVRA 120

Query: 152 AKGKPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATP 211
           A+      + G + + V+   GV  +I PWN+    +A      +V G T+VLKP+   P
Sbjct: 121 AREMVWERQLGSRGRLVHEAVGVCALITPWNWPINQLAAKIGPALVAGCTMVLKPSEIAP 180

Query: 212 VIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAA 271
           + A  F E + E+G P GV N V G+G  +GD L  HP+  +++FTGS   G ++ + AA
Sbjct: 181 LSAQLFAEFIHEAGFPAGVFNMVHGTGPGIGDALTGHPEADMVSFTGSTRAGIQVAKSAA 240

Query: 272 KVQPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEK 331
           +       +KRV  E+GGK   +V  DA +E A        F   GQ C+A +R +V   
Sbjct: 241 ET------VKRVSQELGGKSPNLVFADAGLEAAVTRGVRHCFNNTGQSCNAPTRMLVEAS 294

Query: 332 VYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGGTG 390
           VYD+ +E    + ES     P     ++GPV+ +  +++I   IE G  EG RLV+GG G
Sbjct: 295 VYDEAVEIAKSVAESVQLGDPMEKGPHIGPVVSKVHFERIQKLIEAGIAEGARLVTGGPG 354

Query: 391 ---DDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGA 447
                ++GY+++PTIFAD+  +  + +EEIFGPV+      D  +A+ +AN+T YGL   
Sbjct: 355 RADGFNRGYYVQPTIFADVTNQMTIAREEIFGPVLTMIPFKDEADAVAIANDTPYGLAAY 414

Query: 448 VITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGY-HPFGGFKMSGTDSKAG 497
           V T +     R  ++   G++Y N    GA   Y  PFGG+K SG   + G
Sbjct: 415 VQTGDLDRARRVARQLRAGSVYLN----GAGQEYCSPFGGYKQSGNGREWG 461


Lambda     K      H
   0.316    0.133    0.379 

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: 599
Number of extensions: 32
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: 515
Length of database: 481
Length adjustment: 34
Effective length of query: 481
Effective length of database: 447
Effective search space:   215007
Effective search space used:   215007
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 (21.6 bits)
S2: 52 (24.6 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