GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Cupriavidus basilensis 4G11

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate RR42_RS26255 RR42_RS26255 aldehyde dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS26255
          Length = 499

 Score =  384 bits (987), Expect = e-111
 Identities = 208/476 (43%), Positives = 288/476 (60%), Gaps = 5/476 (1%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTSDPQV 82
           +I+  +  +    TF T++P+T + + +V    ++D+D AV AA  AF S  WS +    
Sbjct: 24  YIDGRWADAADGATFETINPATGKALARVAACGAQDVDRAVAAARKAFQSGVWSDTPRSA 83

Query: 83  RMKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGSV 141
           R   L +L+ LI+ H + LA +E LD GK +  + + D+      +   A   DKI   +
Sbjct: 84  RKATLLRLSHLIETHREELALLETLDMGKPIAETLQYDIPEAGRTYAWYAEAIDKIYDEI 143

Query: 142 IETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201
             TG        REP+GV   ++PWN+PLLMASWK+ P L  G + VLK AE +PL+AL 
Sbjct: 144 APTGPGVLATITREPLGVVAAVVPWNYPLLMASWKVAPALAAGNSVVLKPAEQSPLTALR 203

Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261
           LA L +EAG P GV NVV G G  AG  +  HP +  +AFTGSTATG+  M+ + +SNLK
Sbjct: 204 LAELAEEAGIPAGVFNVVPGLGAAAGQALGRHPDVDCIAFTGSTATGKRFMEYSGQSNLK 263

Query: 262 KVTLELGGKSPNIVFDDA-DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEF 320
           +V LE GGKSP+IVFDD  D+    Q    GIF N GE+C AGSR+YVQ GIYD  + + 
Sbjct: 264 RVWLECGGKSPHIVFDDCPDLDRAAQAAAIGIFSNQGEICIAGSRLYVQSGIYDAFMEKL 323

Query: 321 KNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGER--FGNKGYF 378
           +  A  ++ GDP    T MGA     QL +++ Y+  G+ EGA +  GG+R    + G++
Sbjct: 324 EAHAARMQPGDPLDPATAMGAIVDGAQLQRVMSYVKSGEDEGARLRAGGKRAHTDSGGFY 383

Query: 379 IKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAI 438
           ++PTIF    +   IVR+EIFGPV+ +T+F++ EE I +ANDS YGL +G+ T+NLS A 
Sbjct: 384 MQPTIFECPTQSLTIVREEIFGPVLAVTRFESEEEAIRMANDSPYGLGSGLWTSNLSRAH 443

Query: 439 SVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLS 494
            VS K+ +G +WVN Y D    VPFGG  QSG GR+    ALD YT +K   I L+
Sbjct: 444 RVSRKLQAGLVWVNCYMDSDVTVPFGGVKQSGSGRDKSLHALDKYTDLKTTWISLA 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: 575
Number of extensions: 23
Number of successful extensions: 4
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: 499
Length adjustment: 34
Effective length of query: 461
Effective length of database: 465
Effective search space:   214365
Effective search space used:   214365
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 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