GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Azospirillum brasilense Sp245

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate AZOBR_RS19635 AZOBR_RS19635 succinate-semialdehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS19635 AZOBR_RS19635
           succinate-semialdehyde dehydrogenase
          Length = 485

 Score =  335 bits (858), Expect = 3e-96
 Identities = 188/467 (40%), Positives = 278/467 (59%), Gaps = 10/467 (2%)

Query: 10  YIDGQFVTWRGDAW----IDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPA 65
           Y++G    WR DA+      V NPAT   ++++ D  AE+ R+AI+AA+ A P W A  A
Sbjct: 14  YVNG---VWR-DAFSGKTFAVTNPATGEELAQVADVGAEETRQAINAADAALPAWRAKTA 69

Query: 66  IERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGE 125
            ERA+ LR+    I     +++ L+  E GK    A  EVA+ A +I++ AE  +R  G+
Sbjct: 70  KERAAILRRWFELIMAAQEDLAVLMTLEQGKPLAEARGEVAYGASFIEWFAEEGKRVYGD 129

Query: 126 IIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNA 185
           +I S    + I++ K  +GV   I PWNFP  +I RK+ PAL  G TIV+KP+E TP +A
Sbjct: 130 VIPSFAGNKRIVVLKEPIGVVAAITPWNFPNAMITRKVGPALAAGCTIVVKPAEDTPLSA 189

Query: 186 IAFAKIVDEIGLPRGVFNLVLGRGE-TVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKN 244
           +A A++ +  G+P GVFN+V G     +G EL  +P V  +S TGS   G+ +M  +A  
Sbjct: 190 LALAELAERAGVPAGVFNIVTGSDPVAIGGELTASPIVRKLSFTGSTEVGKILMRQSADT 249

Query: 245 ITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNR 304
           + KV LELGG AP IV DDADL+ AVK  + S+  NSGQ C CA R+ VQ G+YD F  +
Sbjct: 250 VKKVSLELGGNAPFIVFDDADLDEAVKGALASKYRNSGQTCVCANRLLVQAGVYDAFAAK 309

Query: 305 LGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYY 364
           L EA++ ++ GN  E   +  GP+IN  A+E+VE+ +  A+ +GA+VA GGK     G +
Sbjct: 310 LAEAVKQIRVGNGMEAG-VTQGPMINGQAVEKVEELMGDALAKGAKVALGGKRHGLGGTF 368

Query: 365 YPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAM 424
           + PT+L  V  EM +  EE FGPV P+  F+T  DAI MAND+++GL +  Y++++    
Sbjct: 369 FEPTILTGVTTEMRVAREEIFGPVAPLFKFETEADAIRMANDTEFGLAAYFYSRDIGRVW 428

Query: 425 KAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQ 471
           +  + L++G   IN            G ++SGIG    K+G+ ++L+
Sbjct: 429 RVAEQLEYGMVGINEGILSTEVAPFGGIKQSGIGREGSKYGVEDFLE 475


Lambda     K      H
   0.318    0.135    0.392 

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: 561
Number of extensions: 28
Number of successful extensions: 3
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: 479
Length of database: 485
Length adjustment: 34
Effective length of query: 445
Effective length of database: 451
Effective search space:   200695
Effective search space used:   200695
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 (21.7 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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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