GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Azospirillum brasilense Sp245

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate AZOBR_RS29185 AZOBR_RS29185 aldehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS29185 AZOBR_RS29185 aldehyde
           dehydrogenase
          Length = 478

 Score =  253 bits (647), Expect = 8e-72
 Identities = 157/459 (34%), Positives = 233/459 (50%), Gaps = 16/459 (3%)

Query: 56  NPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEF 115
           NPAR  +++G  + A+ + AE+A+ +A  A   W   NP+ R+++L +    +  R  E 
Sbjct: 23  NPARPGEVIGHYAWASVEQAEEALGAAHAALPGWAASNPQTRSDVLRRVGDELNARAEEL 82

Query: 116 SAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILS--RPGEQNRYFYTPMG 173
            A L  E GK  +E   +   +     Y A +   L +G E L   R G        P+G
Sbjct: 83  GALLTREEGKTLREGIGEVRRSAQIFHYAAGE--PLRQGGEALPGLRDGTTAMVSREPVG 140

Query: 174 VTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINY 233
           V V I+PWNF +A+        +  GNTVVLKP+  TP  A +  ++L  AGLP G  N 
Sbjct: 141 VVVLITPWNFPMAVPAWKTAYALAFGNTVVLKPSEVTPACAWELADILHRAGLPAGAFNL 200

Query: 234 VPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTV 293
           V G G  +G  LVD      ++FTGS  VG  + ER+         + RV +E+GGK+ +
Sbjct: 201 VVGDGRTLGPALVDG--ADAVSFTGSPGVGRAILERSVA------RMTRVQLELGGKNPL 252

Query: 294 VVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPT 353
           VV  DADL+LA +  L  AF  +GQ+C+A SR ++ + V+D  +E+ V     L VGDP 
Sbjct: 253 VVHDDADLELAVDIALQGAFHSTGQRCTATSRIIVDRRVHDAFVERLVTRIAALRVGDPM 312

Query: 354 NRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGGEGDSSTGFFIQPTIIADLDPEAVI 412
           +    MGPV+ E    K +  I   + EG  L  GG      G+F++PT+    D    I
Sbjct: 313 DAATDMGPVVSEAQLAKDLHCIADARSEGAELAFGGGRMDGDGYFLEPTLFVGTDNAMRI 372

Query: 413 MQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNR 472
            ++E+FGPV     A+  DHA+ IAN++++ L+  ++TR  A  E  +R    G +  N 
Sbjct: 373 NRDEVFGPVACVIPADGLDHAIAIANDSDHALSSGIVTRGLASAETFRRRSRAGLVMVNA 432

Query: 473 NCTGAIVGYH-PFGGFKMSGTDSKAGGPDYLALHMQAKT 510
              G  + YH PFGG   SG   +  G   +    + KT
Sbjct: 433 PTAG--IDYHVPFGGRGPSGYGGREQGSAAVEFFTEGKT 469


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: 596
Number of extensions: 29
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: 478
Length adjustment: 34
Effective length of query: 481
Effective length of database: 444
Effective search space:   213564
Effective search space used:   213564
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 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