GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Azospirillum brasilense Sp245

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate AZOBR_RS32475 AZOBR_RS32475 aldehyde Dehydrogenase

Query= BRENDA::A0A0H3W5K4
         (859 letters)



>FitnessBrowser__azobra:AZOBR_RS32475
          Length = 475

 Score =  238 bits (607), Expect = 6e-67
 Identities = 147/446 (32%), Positives = 244/446 (54%), Gaps = 16/446 (3%)

Query: 11  QKQIDLLVSRAQEAQKKFMSYTQEQIDAIVKAMALAGVD--KHVELAKMAYEETKMGVYE 68
           Q+ I  LV+RA+ AQ+ F   TQE++D  V A+A A  +  +   LA++A  +T +G   
Sbjct: 15  QEAIAALVARARTAQRAFADATQERVDDAVAALAWAIYEPGRARALAELAVADTGLGNVA 74

Query: 69  DKITKNLFATEYVYHDIKNEKTVGIINENIEENYMEVAEPIGVIAGVTPVTNPTSTTMFK 128
           DKI KN   T     D+   +TVG+I E+  +  +++A+P+GV+  VTP TNP +T + K
Sbjct: 75  DKIVKNQRKTFGTLRDLMRVRTVGVIEEDTAKGIVKIAKPLGVVGAVTPSTNPAATPVNK 134

Query: 129 CLISIKTRNPIIFSFHPKAIKCSIAAAKVMYEAALKAGAPEGCIGWIETPSIEA-TQLLM 187
            ++++K RN II +  P     +    ++M     + GAPE  +  I TP  +  TQ LM
Sbjct: 135 AMMAVKGRNAIIIAPSPMGSAATGRTVELMRAELARIGAPEDLVQMIPTPITKGLTQALM 194

Query: 188 THPGVSLILATGGAGMVKAAYSSGKPALGVGPGNVPCYIEKSANIKRAVSDLILSKTFDN 247
               V L++ TG    V+ AYSSG PA+GVG GNVP  +++SA++  A   +  SKTFDN
Sbjct: 195 --EAVDLVVVTGSQDNVRRAYSSGTPAIGVGAGNVPVIVDESADLAEAARKIGASKTFDN 252

Query: 248 GVICASEQAVIIDEEIADEVKKLMKEYGCYFLNKDEIKKL-----EKFAIDEQSCAMSPA 302
              C+SE A+++ + + D     ++E G +    +E +++     E   ++ +  A  PA
Sbjct: 253 STSCSSENALVVLDSVYDATIAALEEAGAHLCTPEERERVQSRLWENGKLNRKLIAKDPA 312

Query: 303 VVGQPAAKIAEMAGFKVPEGTKILVAEYEGVGPKYPLSREKLSPILACYTVKDYNEGIKK 362
           ++ + A ++A  A        +  + E  GVG  +P S EKLS +LA Y V D++  + +
Sbjct: 313 ILAE-AFELAPKA-----REARFFLVEETGVGKAHPFSGEKLSLVLAVYRVPDFDAAVDQ 366

Query: 363 CEEMTEFGGLGHSAVIHSENQNVINEFARRVRTGRLIVNSPSSQGAIGDIYNTNTPSLTL 422
             ++ +  G GHS  IH+ ++      A  +   R++VN   + G  G   +    +L++
Sbjct: 367 VRKILDHQGRGHSCGIHTRDEAHAKRLADELDVVRVLVNFAHTFGNGGGFDSGLNFTLSM 426

Query: 423 GCGSMGRNSTTDNVSVKNLLNIKRVV 448
           GCGS  +NS ++N+S K+ +NI  +V
Sbjct: 427 GCGSWQKNSISENLSWKHFVNITHLV 452


Lambda     K      H
   0.317    0.134    0.382 

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: 784
Number of extensions: 42
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: 859
Length of database: 475
Length adjustment: 38
Effective length of query: 821
Effective length of database: 437
Effective search space:   358777
Effective search space used:   358777
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: 54 (25.4 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