GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Sphingomonas koreensis DSMZ 15582

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases

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



>FitnessBrowser__Korea:Ga0059261_1680
          Length = 469

 Score =  275 bits (702), Expect = 3e-78
 Identities = 158/456 (34%), Positives = 244/456 (53%), Gaps = 6/456 (1%)

Query: 36  KTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLID 95
           +TF  + P+T         A + D+D AV AA  AF   W+ +  + R   +  +AD I+
Sbjct: 17  ETFPVIDPATGRPFADAPLASTADLDAAVAAARRAF-PGWAATPIEDRAAAILAIADSIE 75

Query: 96  EHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRRE 155
              D LA + + + GK +  + G++    A+ R+ AG    +   V++  D+      R+
Sbjct: 76  AAKDELARLLSAEQGKPVPNAVGEIMGALAWARATAGLRPAV--DVLKDDDSVRVEVHRK 133

Query: 156 PIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGV 215
           P+GV   I PWNFP+++A W + P L  G T V+K +  TPL+AL +   I  A  PPGV
Sbjct: 134 PLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAALRMVE-IANAHLPPGV 192

Query: 216 VNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIV 275
           +N V+G     G  I+SHP I K+ FTGST TGR IM   A +NLK++TLELGG    IV
Sbjct: 193 LNSVTG-EVEIGRAIASHPGIDKIVFTGSTPTGRSIMADGA-ANLKRLTLELGGNDAAIV 250

Query: 276 FDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKE 335
             DADV      +    F N+G++C A  R+YV E I+D +  +    A +  +G     
Sbjct: 251 LPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAEKLAEMARTAVVGPGSDA 310

Query: 336 DTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQIVR 395
            +  G   ++ Q D +    D  +  G   + GGE     GYF   ++  DV +  +IV 
Sbjct: 311 ASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREGDGYFFPLSVVVDVTDGMRIVD 370

Query: 396 DEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYN 455
           +E FGP++ + ++   E+ +A AN +E GL   V + + + A++ + ++ +GT+WVN + 
Sbjct: 371 EEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAFAQRLEAGTVWVNDHA 430

Query: 456 DFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491
              P VPFGG  QSG+G E G   L+ Y Q++ VR+
Sbjct: 431 SISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTVRV 466


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: 560
Number of extensions: 29
Number of successful extensions: 6
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: 469
Length adjustment: 34
Effective length of query: 461
Effective length of database: 435
Effective search space:   200535
Effective search space used:   200535
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