GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Nocardioides daejeonensis MJ31

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_110207251.1 DNK54_RS12190 aldehyde dehydrogenase family protein

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_003194585.1:WP_110207251.1
          Length = 474

 Score =  252 bits (643), Expect = 2e-71
 Identities = 165/459 (35%), Positives = 232/459 (50%), Gaps = 10/459 (2%)

Query: 41  INGE-RVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAA 99
           + GE R  T + I S NPA   EVV     A+ +   +A+ AA KA + WR T   ERAA
Sbjct: 9   VGGEWRAGTGSAIESRNPARPHEVVASGHAATPDDVTEAVAAATKAAQAWRRTLMHERAA 68

Query: 100 VLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNS 159
           VL R A  +  R       L  E GK   E   +   A +   + A Q          + 
Sbjct: 69  VLRRTAELLEERADALGLELTLEEGKTLVEGIGEVRRAAEIFRFNAGQADREVGEVFASP 128

Query: 160 REGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVE 219
           R GE+      P GV  VI PWNF  AI A      ++ GN VV KPAS  P++A +  E
Sbjct: 129 RRGERIVVTRKPIGVVAVITPWNFPIAIPAWKIAPALIHGNAVVWKPASIVPLLAVRLAE 188

Query: 220 VLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQH 279
            L ++GLP GV++ + G GA +G  +   P    +TFTGS  +GT + +  A ++     
Sbjct: 189 ALHDAGLPAGVLSLIIGPGA-LGSQIASAPGVHAVTFTGSTGIGTGLLQLCAPLR----- 242

Query: 280 LKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLER 339
            + V AEMGGK+  VV  DAD+ELAA  I   A    GQKC+A SR VV + V + +   
Sbjct: 243 -RPVQAEMGGKNAAVVFADADLELAADQIVLGAMRSTGQKCTATSRLVVEDSVAEDLRTL 301

Query: 340 VIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEGRLVSGGTGDDSKGYFIK 399
           +++  E+ V      +DV +GPV   G+  +I S I+   + G  V         G+++ 
Sbjct: 302 LVQRIEALVVGDGTRSDVTVGPVSSGGAQAEITSMIDDALRGGARVVAQAEAPDDGHYVP 361

Query: 400 PTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHIERA 459
           PTI  ++D +  + +EE+FGPV+A    +D D  LE+AN +E+GL+ AV T++     R 
Sbjct: 362 PTIL-EVDVRQPIWREEVFGPVLAMTTGADEDRVLELANASEFGLSAAVFTSDLSRTLRI 420

Query: 460 KQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGG 498
             E  VG L+ N    GA   + PFGG K SG   K  G
Sbjct: 421 MDELEVGVLHVNSESAGA-DPHVPFGGVKDSGIGPKEQG 458


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: 587
Number of extensions: 31
Number of successful extensions: 6
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: 474
Length adjustment: 34
Effective length of query: 481
Effective length of database: 440
Effective search space:   211640
Effective search space used:   211640
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