GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Azospirillum brasilense Sp245

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate AZOBR_RS22315 AZOBR_RS22315 aldehyde dehydrogenase

Query= metacyc::MONOMER-16244
         (495 letters)



>FitnessBrowser__azobra:AZOBR_RS22315
          Length = 497

 Score =  316 bits (810), Expect = 1e-90
 Identities = 184/477 (38%), Positives = 270/477 (56%), Gaps = 10/477 (2%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           F   EF  + S K F  V+P+T E + +     + D+D AV AA AA    W+    + R
Sbjct: 23  FFGGEFRPASSGKGFPVVNPATGETVAEAAFGEAADVDAAVAAAVAA-QKEWAKRPVRER 81

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLMC-SKGDVALTAAYFRSCAGWTDKIKGSVI 142
            K++ +   ++D H + +A + AL+ GK+L   S+ +  + +  F    G   ++KG  I
Sbjct: 82  GKLVAECGRVLDAHKEEIAKLIALETGKALRTESRVEAGVLSDAFVFFGGLAPELKGETI 141

Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
               +    T REP+GV G IIPWN PLL+ + K+ P +  G   V+K+AE  PL+ L +
Sbjct: 142 PFNPSMLTMTVREPVGVVGAIIPWNVPLLLMALKIAPAMVAGNAVVVKSAEEAPLAVLRV 201

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
             LI     P GVVN++SG+GP  GAP+ +H  +KKV FTGS  TG+ + K AAE  L  
Sbjct: 202 VQLINTV-IPAGVVNILSGYGPECGAPLVAHKDVKKVTFTGSVETGKIVYKTAAEK-LIP 259

Query: 263 VTLELGGKSPNIVFDDADVKSTIQHLVTGI-FYNTGEVCCAGSRIYVQEGIYDKIVSEFK 321
           VTLELGGKSP IV  DAD+   I   + G+ F   G+ C A SRI+V + I+D  V + K
Sbjct: 260 VTLELGGKSPMIVCGDADLDQAIAGAIAGMRFTRQGQSCTASSRIFVHDSIHDAFVEKLK 319

Query: 322 NAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN----KGY 377
               ++K+GDP  E T +G   S  QLD++  YI IGK+ GAT         +    KG 
Sbjct: 320 EKVNAMKMGDPLDESTDIGTIVSPQQLDRVQSYIAIGKEGGATPHVCSAMPSDPKLTKGL 379

Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437
           +++P IF  VK   +I ++EIFGPV  + ++   EEVIA AND+EYGLAA + T +L  A
Sbjct: 380 YVQPHIFTGVKNSDRIAQEEIFGPVCCVIRWTDYEEVIAQANDTEYGLAATIWTRDLKVA 439

Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEA-LDNYTQVKAVRIGL 493
           +   +++ +G + VN      P + +GG   SG+G+E   EA L+++T  K + I +
Sbjct: 440 MDAVHRLEAGFVQVNQNLVVQPNLSYGGVKSSGLGKEASLEAMLEHFTHKKTIIINM 496


Lambda     K      H
   0.316    0.133    0.389 

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: 593
Number of extensions: 35
Number of successful extensions: 7
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: 495
Length of database: 497
Length adjustment: 34
Effective length of query: 461
Effective length of database: 463
Effective search space:   213443
Effective search space used:   213443
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