GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Gracilibacillus halophilus YIM-C55.5

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_003471449.1 J416_RS11040 aldehyde dehydrogenase family protein

Query= curated2:Q9K5Z5
         (515 letters)



>NCBI__GCF_000359605.1:WP_003471449.1
          Length = 473

 Score =  262 bits (670), Expect = 2e-74
 Identities = 162/470 (34%), Positives = 252/470 (53%), Gaps = 21/470 (4%)

Query: 37  YPLVINGERVTTDDKIVSVNPAMKEQVIGVVSKASREIVDDAFKSAETAFHTWKNVNPEE 96
           Y L ING  V T++ I  V     +     V+KASRE VD+A  SA  A+     ++P +
Sbjct: 4   YALYINGGWVETEETI-DVLDKYSQTTYATVAKASREHVDEAISSATKAYRK-NQLSPYQ 61

Query: 97  RANILIRAAAIIRRRKHEFSAWLVKEAGKPWKEADADTAEAIDFLEYYARQMITLK-DGK 155
           R  IL   + +++  K E +  + KEAGKP K+A  +   + +     A +   +  +G 
Sbjct: 62  RFEILRNVSTLMKNNKEELAYTITKEAGKPLKQARTEIDRSAETFLLAAEEAKRIHGEGV 121

Query: 156 PVNSREGEHNRYFYT---PIGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPV 212
           PV +  G  +R  +T   P+GV   ISP+NF L ++A      +  GN V+LKPAS TP+
Sbjct: 122 PVEAAPGSEHRMAFTIKVPVGVVGAISPFNFPLNLVAHKVAPALAAGNAVVLKPASKTPL 181

Query: 213 VAAKFVEVLEEAGLPKGVVNFVPGSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAAV 272
            + K  ++LEEAGLPKG++  V GSG+ +G  ++D  +  L TFTGS +VG++L +    
Sbjct: 182 ASLKLAKLLEEAGLPKGLLQVVVGSGSVVGQQMMDDERIDLYTFTGSAEVGLQLKQNTG- 240

Query: 273 VHPGQQHLKRVIVEMGGKDTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDV 332
                  L R+I+E+G    V+VDK+AD+D AA+++   +F F+GQ C +  R  +H+ +
Sbjct: 241 -------LNRLILELGNNSPVIVDKEADIDHAAKTLAGQSFAFAGQVCISVQRVYVHESI 293

Query: 333 YDVVLEKAVALTKQLSVGEPTAPDVYMGPVVDQGAFSKIMSYIEVGKEEG-RLMVGGEGD 391
            +  LE      KQL VG+PT     +GP++      +  ++I    ++G ++++GG+  
Sbjct: 294 QERFLETFSEQIKQLLVGDPTDATTDVGPMISVSEAERAETWIHEAVDKGAKVVLGGK-- 351

Query: 392 DSKGFFIQPTIFADVDPHARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVITT 451
             +G  ++PTI  DV P  R++ EEIF PVV+     D D  +E  N + YGL G + T 
Sbjct: 352 -REGALLEPTILTDVKPEMRVVCEEIFAPVVSVIAYTDLDSCIEEVNQSVYGLQGGIFTQ 410

Query: 452 NRHHIEKAKRDFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDY 501
           N      A +   VG    N + +   V   P+GG K SG   +  GP Y
Sbjct: 411 NIDTAYYAAKRVEVGGFMIN-DGSQYRVDLMPYGGVKDSGNGKE--GPKY 457


Lambda     K      H
   0.318    0.135    0.394 

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: 558
Number of extensions: 21
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: 473
Length adjustment: 34
Effective length of query: 481
Effective length of database: 439
Effective search space:   211159
Effective search space used:   211159
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 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