GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Acidovorax sp. GW101-3H11

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate Ac3H11_612 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= SwissProt::P94391
         (515 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_612 2-ketoglutaric
           semialdehyde dehydrogenase (EC 1.2.1.26)
          Length = 483

 Score =  257 bits (657), Expect = 6e-73
 Identities = 161/475 (33%), Positives = 236/475 (49%), Gaps = 13/475 (2%)

Query: 40  VINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAA 99
           +ING         +S NP+D  EVV   ++A +   E A++AAA A   W  ++P+ RA 
Sbjct: 13  LINGRWEIGTTTGISTNPSDTREVVAEYARADRNQTELAVRAAADALPTWSQSTPQRRAD 72

Query: 100 VLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNS 159
           VL    +++  RK E  ALL +E GK   E  A+ A +    +++A + + +      + 
Sbjct: 73  VLDMIGSELLARKDELGALLAREEGKTLPEGVAEVARSGQIFKFFAGEALRIQGELLASV 132

Query: 160 REGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVE 219
           R+G +      P GV  +I PWNF FAI A      +  GNTVV KPA   P       E
Sbjct: 133 RQGVQVDVTREPVGVVGIIAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPACGWALAE 192

Query: 220 VLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQH 279
           ++  SGLP G  N + GSG EVG  LVDHP  + ++FTGS   G RI   A+      Q 
Sbjct: 193 IISRSGLPAGAFNLIMGSGREVGQTLVDHPLVNALSFTGSVATGDRILRAAS------QR 246

Query: 280 LKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLER 339
             +V  EMGGK+ ++V  DAD++ A       ++   GQ+C+A SR +V  +V+D  + R
Sbjct: 247 RAKVQLEMGGKNPLIVLADADLDQAVDCALQGSYFSTGQRCTASSRLIVEAEVHDAFVAR 306

Query: 340 VIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGGTGDD--SKGY 396
           +     S            MGPV+D     + + YI+I K EG   V GG   +  + G+
Sbjct: 307 LRNRLASLKVGHALERGTEMGPVVDDNQLAQNLGYIDIAKSEGAEHVWGGERLERPTPGH 366

Query: 397 FIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHI 456
           ++ P +F    P+ R+ +EEIFGPV    +  D+D AL +AN+T +GL   + T + K  
Sbjct: 367 YMSPALFL-ARPEHRVAREEIFGPVACVLRADDYDHALALANDTPFGLCAGICTTSLKRA 425

Query: 457 ERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGGPDYLALHMQAKT 510
              K+   VG    N    G  V +H PFGG K S   ++  G      +   KT
Sbjct: 426 MHFKRHAAVGMTMVNLPTAG--VDFHVPFGGRKESSYGAREQGRYAAEFYTTVKT 478


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: 549
Number of extensions: 33
Number of successful extensions: 4
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: 483
Length adjustment: 34
Effective length of query: 481
Effective length of database: 449
Effective search space:   215969
Effective search space used:   215969
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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