GapMind for catabolism of small carbon sources

 

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

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_040513649.1 J416_RS13265 betaine-aldehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>NCBI__GCF_000359605.1:WP_040513649.1
          Length = 484

 Score =  245 bits (626), Expect = 2e-69
 Identities = 143/466 (30%), Positives = 243/466 (52%), Gaps = 23/466 (4%)

Query: 41  INGERVTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQT--WRNVNPEERA 98
           +N +   T D I  +N     +++ +  + ++  A+ AI +A +AF    W+N +  ER 
Sbjct: 8   VNAQSGNTRDIINPYN----QEVIATAVEGDESDAKAAIAAARQAFDQGDWKNTSATERG 63

Query: 99  NILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEIL 158
            I+ K A  I R K E +     + GK  +E+  D  +      YYA   I    G EI+
Sbjct: 64  KIVRKIADFIERDKEELAYLESLDTGKTVEESRGDMDDIAGVFHYYAE--IADKDGGEII 121

Query: 159 SRP--GEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAK 216
             P     ++  + P+GV   I+PWN+ L          +VTGNT+++KP+  TP+   K
Sbjct: 122 ESPLPNSISKVVHEPVGVCGQITPWNYPLLQASWKLAPALVTGNTLIMKPSEITPLTTVK 181

Query: 217 FVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPG 276
             +++E+AG+P GV N V G+G+  G  L +     LI+FTG    G ++ + A      
Sbjct: 182 VFKLIEEAGVPAGVANLVLGAGSTTGAELSESKDVDLISFTGGIATGKKIMKAAT----- 236

Query: 277 QNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEV 336
            +++K+  +E+GGK+  ++  D D + A +  +   F  +GQ CSAG+R ++ + ++D+ 
Sbjct: 237 -DNVKKTALELGGKNPNIIFADTDFETAVDQAMNGVFFHAGQICSAGTRLIVEESIHDQF 295

Query: 337 LEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEGRLMTGG-----EGD 391
           +E  V   KN+ +G   + D  MGP+I ++   K++ Y+E GKKEG  +  G     + +
Sbjct: 296 VEALVNRVKNIKLGSGFDDDTQMGPLISKEHLNKVIDYVETGKKEGVTVEVGGKQPEDPE 355

Query: 392 SSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITR 451
              GFF  PT++     +  ++QEE FGPV+   K +  D A+++AN++ YGL GAV T 
Sbjct: 356 LQDGFFYLPTVLTGCTTDMDVVQEEGFGPVITVEKFSTEDEAVQLANDSIYGLAGAVFTN 415

Query: 452 NRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAG 497
           N A  E+  +   +G ++ N         + P+GG+K SG   + G
Sbjct: 416 NIAKAERCAQAMRMGTVWINE--MNVYFPHAPWGGYKQSGIGRELG 459


Lambda     K      H
   0.316    0.134    0.388 

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: 638
Number of extensions: 35
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: 484
Length adjustment: 34
Effective length of query: 481
Effective length of database: 450
Effective search space:   216450
Effective search space used:   216450
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