GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_612
          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.

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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