GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Lutibaculum baratangense AMV1

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_023433101.1 N177_RS14415 aldehyde dehydrogenase

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



>NCBI__GCF_000496075.1:WP_023433101.1
          Length = 492

 Score =  360 bits (925), Expect = e-104
 Identities = 202/480 (42%), Positives = 284/480 (59%), Gaps = 6/480 (1%)

Query: 19  QPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHS-SWST 77
           +P   +I+  F +  +  +F +V P+T E    +  A + D+D AV AA  AFH  SWS 
Sbjct: 4   EPFRNYIDGAFCEGGAG-SFESVDPATGEAWANMPAANAADVDRAVRAADRAFHDPSWSR 62

Query: 78  SDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKI 137
                R K+LY+LADL+ E+A  LA +E  D GK +  +   +A  A Y+R  AG  DKI
Sbjct: 63  LTATQRGKLLYRLADLVAENAQALAELETRDTGKIIRETSAQIAYVADYYRYYAGLADKI 122

Query: 138 KGSVIETGDTHFN-YTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTP 196
           +G+ +         Y RREPIGV   ++PWN  L +++ KLGP L  GCT VLK +E  P
Sbjct: 123 EGAHLPIDKPDMETYLRREPIGVVAAVVPWNSQLFLSAVKLGPALAAGCTVVLKASEDGP 182

Query: 197 LSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAA 256
              L  A L+ +AG PPGVVN+++GFG   G+ ++SHP + ++AFTG  AT RHI++ +A
Sbjct: 183 APLLAFARLVDQAGFPPGVVNILTGFGDQCGSALASHPLVARIAFTGGPATARHIVRHSA 242

Query: 257 ESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316
           E NL  VTLELGGKSP +VF+DAD+ S    +V GIF  TG+ C AGSR+ VQ GI D +
Sbjct: 243 E-NLAAVTLELGGKSPVVVFEDADLDSVANAVVAGIFAATGQSCVAGSRLIVQRGIKDAL 301

Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN-- 374
           +      A +++IGDP  ++T MG   +  QL  I   I      G  ++TGG R     
Sbjct: 302 LERLVQKARAIRIGDPQAQETEMGPLATARQLRHIEDVIARSLAAGGRLVTGGGRPDGFP 361

Query: 375 KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNL 434
            G++ +PTI          V +E+FGPV+++  F+   E +  AN + YGLA+GV T +L
Sbjct: 362 AGHYFEPTIIDCDATTIPSVEEELFGPVLSVLGFEEETEAVEFANRTPYGLASGVFTASL 421

Query: 435 STAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLS 494
           + A  +   I +G +WVNTY    P++PFGGY  SG GRE G +A  +YT+ KAV I +S
Sbjct: 422 TRAHRMIRAIRAGVVWVNTYRAVSPIMPFGGYGLSGSGREGGLDAALDYTRTKAVWIRVS 481


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: 598
Number of extensions: 27
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.

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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