GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Methylocystis bryophila S285

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein

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



>NCBI__GCF_002117405.1:WP_085772038.1
          Length = 506

 Score =  352 bits (904), Expect = e-101
 Identities = 209/500 (41%), Positives = 287/500 (57%), Gaps = 23/500 (4%)

Query: 10  KLPNGTTYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATA 69
           KL      ++    FI  ++V     + F  +SP T   I QV    + D++ A++AA  
Sbjct: 8   KLKGSVAIKKRYDNFIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHK 67

Query: 70  AFHSSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFR 128
           A   +W  +    R  +L K+A  +D++   LA +E +DNGK +   +  D+ L   +FR
Sbjct: 68  A-KDAWGKTPAAERANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFR 126

Query: 129 SCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTV 188
             AG     +GS+ E       Y   EP+GV GQIIPWNFP+LMA+WKL P L  G   V
Sbjct: 127 YFAGCLRAQEGSLSEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVV 186

Query: 189 LKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATG 248
           LK AE TP+S L +A LI +   PPGV+N+V+GFG  AG P++S+ +I K+AFTG T TG
Sbjct: 187 LKPAEQTPMSILAVAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTG 245

Query: 249 RHIMKAAAESNLKKVTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVCCA 302
           R IM+ AAE NL  VTLELGGKSPNI F      DDA +   ++   +    N GEVC  
Sbjct: 246 RLIMQYAAE-NLIPVTLELGGKSPNIFFADVMAEDDAFLDKALEGFAS-FALNQGEVCTC 303

Query: 303 GSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEG 362
            SR  VQ  IYDK + +       ++ G P    T +GAQ S  QL+KIL Y+DIG+KEG
Sbjct: 304 PSRALVQRSIYDKFMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEG 363

Query: 363 ATVITGGERFG-----NKGYFIKPTIFGDVKEDH---QIVRDEIFGPVVTITKFKTVEEV 414
           A V+ GGER        +GY+++PT      E H   ++ ++EIFGPVV++T F+T EE 
Sbjct: 364 AKVLIGGERSVLEGELKEGYYMQPTAL----EGHNRMRVFQEEIFGPVVSVTTFETEEEA 419

Query: 415 IALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGRE 474
           + +AND+ YGL AG+ T + S A      I +G +W N Y+ +     FGGY QSGIGRE
Sbjct: 420 LQIANDTLYGLGAGLWTRDGSRAYRCGRAIRAGRVWTNCYHAYPAHAAFGGYKQSGIGRE 479

Query: 475 MGEEALDNYTQVKAVRIGLS 494
             +  LD+Y Q K + +  S
Sbjct: 480 NHKMMLDHYQQTKNLLVSYS 499


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: 576
Number of extensions: 31
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: 506
Length adjustment: 34
Effective length of query: 461
Effective length of database: 472
Effective search space:   217592
Effective search space used:   217592
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 Apr 09 2024. 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