GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Brucella inopinata BO1

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_008509302.1 BIBO1_RS15485 aldehyde dehydrogenase

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



>NCBI__GCF_000182725.1:WP_008509302.1
          Length = 492

 Score =  342 bits (876), Expect = 2e-98
 Identities = 193/479 (40%), Positives = 275/479 (57%), Gaps = 6/479 (1%)

Query: 20  PTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHS-SWSTS 78
           P  LFIN  +  +        +SP    ++T +  A + D+D A  AA  +F   +W+ +
Sbjct: 15  PQSLFINGRWQPAADGNVMAVISPIDGTQLTTIAAATAIDVDRAAAAARQSFEKGTWAKA 74

Query: 79  DPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSL-MCSKGDVALTAAYFRSCAGWTDKI 137
            P  R KVL K+A+LI+ +A  LA +   DNG  + M  K +    A  FR  A   DK+
Sbjct: 75  APAERRKVLLKIAELIERNALELAVLGVRDNGTEISMALKAEPGSAANSFRYYAEAIDKV 134

Query: 138 KGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPL 197
            G +  T +       R P+GV G I+PWNFP+++ +WK+ P L  G + VLK AE   L
Sbjct: 135 YGEIAPTAENILGLVHRAPVGVVGAIVPWNFPMMIGAWKIAPALAAGNSIVLKPAEGASL 194

Query: 198 SALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAE 257
           S L LA L  EAG P GV+NVV+G GP  G  +  HP I  +AFTGS   GR +++ +A 
Sbjct: 195 SLLRLAELCAEAGLPEGVLNVVTGAGPVTGEALGLHPDIDVLAFTGSGFVGRKLLEYSAR 254

Query: 258 SNLKKVTLELGGKSPNIVFDDA-DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316
           SNLK+V LELGGKSPNIVF DA D+    +    GIF N+G+VC AGSR+ V+  I  + 
Sbjct: 255 SNLKRVYLELGGKSPNIVFADAPDLAQAAKVSAYGIFRNSGQVCVAGSRLLVERSIAGEF 314

Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNK- 375
             +    A ++K+GDP    T  GA +S++QL K L + +    EGA + TGG+R   + 
Sbjct: 315 AEKVSAIAAAIKVGDPLNLATEAGAISSEVQLRKNLGFAEQALSEGAGLRTGGKRILEET 374

Query: 376 -GYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNL 434
            G++++PT+F +V+    + R+E+FGP+++I  F   E+ + +ANDS+YGLA+ V T+NL
Sbjct: 375 GGFYMQPTVF-NVEPGMTLAREEVFGPILSIIPFDNEEDALKIANDSDYGLASAVWTSNL 433

Query: 435 STAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493
           S A  +   I +G + VNTY      VP GG  QSG G +    ALD Y  +K   I L
Sbjct: 434 SRAHRMVRGIRAGVVHVNTYGGADNTVPLGGVKQSGNGHDKSLHALDKYIDLKTAWIQL 492


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: 540
Number of extensions: 28
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: 495
Length of database: 492
Length adjustment: 34
Effective length of query: 461
Effective length of database: 458
Effective search space:   211138
Effective search space used:   211138
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 24 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:

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