GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Methylocella silvestris BL2

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_012592396.1 MSIL_RS17445 aldehyde dehydrogenase family protein

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



>NCBI__GCF_000021745.1:WP_012592396.1
          Length = 474

 Score =  319 bits (818), Expect = 1e-91
 Identities = 177/456 (38%), Positives = 263/456 (57%), Gaps = 6/456 (1%)

Query: 34  SKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADL 93
           S  TF   +P+TEE I    +A  E ++ AV AA  AF  +WS      R  ++ ++ DL
Sbjct: 20  SAATFEAFNPATEEVIAAAPDASREQLEAAVAAAKRAF-PAWSARPIAERQALVARIGDL 78

Query: 94  IDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTR 153
           I+ HA+    +   + GK    ++ ++  +A + R  A    ++   + E   T    TR
Sbjct: 79  IEAHAEDFMRLLTREQGKPRKGAEWEIFGSAIWCREIA--KQELPVHISEESQTRRVETR 136

Query: 154 REPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPP 213
           REP+GV   I PWNFP+L+A WK+ P L  G T VLK +  TPL  L L  L++E   PP
Sbjct: 137 REPLGVIAGITPWNFPVLLAIWKIAPALVAGNTMVLKPSPYTPLCTLKLGELVREL-LPP 195

Query: 214 GVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPN 273
           GV+N+VSG G   G  +++H  I+K++FTGST TGR IM AAA  N+K++TLELGG  P 
Sbjct: 196 GVLNIVSG-GNELGVWMTTHSDIRKISFTGSTETGRKIM-AAASGNIKRITLELGGNDPA 253

Query: 274 IVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPF 333
           IV  D DVK T + L    F N+ + C A  R+Y+   IYD + +E    A+++K+GD  
Sbjct: 254 IVLPDVDVKETAEKLFWAAFQNSAQFCVAAKRLYIHADIYDDLAAELVAYAKTVKVGDGS 313

Query: 334 KEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQI 393
            + T +G   +++Q +K+   +   K  G   + GG+    KG+F+  TI  +  E+ ++
Sbjct: 314 LQGTDLGPIQNRMQFEKLKNLLADAKTNGLRFLLGGDVTDAKGFFVPVTIIDNPPENSRV 373

Query: 394 VRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNT 453
           V +E FGP++ + KF  ++ VIA AND+EYGLAA V   ++  A  V+ +I++GT+WVN 
Sbjct: 374 VAEEAFGPILPLLKFDDIDGVIARANDTEYGLAASVWGKDIKAARRVAERIDAGTVWVNE 433

Query: 454 YNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489
            + F P V FGG+ QSG+G E   E L  YT  K +
Sbjct: 434 VHTFSPHVAFGGHKQSGLGIENALEGLAEYTNAKTL 469


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: 510
Number of extensions: 20
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: 474
Length adjustment: 34
Effective length of query: 461
Effective length of database: 440
Effective search space:   202840
Effective search space used:   202840
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