GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA 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)



>FitnessBrowser__azobra:AZOBR_RS29185
          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 (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