GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Luteipulveratus mongoliensis MN07-A0370

Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_052591396.1 VV02_RS10095 aldehyde dehydrogenase family protein

Query= SwissProt::O34660
         (495 letters)



>NCBI__GCF_001190945.1:WP_052591396.1
          Length = 485

 Score =  432 bits (1110), Expect = e-125
 Identities = 228/469 (48%), Positives = 309/469 (65%), Gaps = 9/469 (1%)

Query: 16  LQGTKKLYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEW 75
           LQ +  L+I+G+FV   +G++F T NPAT E L  + EA A DVDKAVKAAR A+ +  W
Sbjct: 18  LQSSYGLFINGEFV-DGTGSSFKTINPATEEKLADVSEASADDVDKAVKAARTAYTR-VW 75

Query: 76  RTMSPASRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWC 135
             MS A R + ++++A +M+E   ELA LE+LDNGKPI E+ + D+P A  H  Y+AGW 
Sbjct: 76  SRMSGAERGKYVFRIARIMQERARELAVLESLDNGKPIKESRDVDVPTAAAHFFYHAGWA 135

Query: 136 TKITGQTIPVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQ 195
            K+    +  +G+        P+GVVGQ+IPWNFPLLM  WK+  ALATG T+VLKPAE 
Sbjct: 136 DKLEYAGLSPAGS----PPPRPLGVVGQVIPWNFPLLMLAWKIAPALATGNTVVLKPAET 191

Query: 196 TPLSALYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMST 255
           TPL+AL  AE+  QA  P GV+NI+ G G   G+AL  H  VDKIAFTGST++GK I  +
Sbjct: 192 TPLTALLFAEICQQADLPPGVVNIVTGAGA-TGQALVEHPDVDKIAFTGSTDVGKAIARS 250

Query: 256 AAKSIKRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDE 315
            A + KR TLELGGK+ NI+  DA + +A+ G +NG+ FNQG VCCAGSR+ + +   DE
Sbjct: 251 IAGTRKRATLELGGKAANIVFEDAAIDQAVEGIVNGIFFNQGHVCCAGSRLLVQESVADE 310

Query: 316 VVDEMASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCPFEA 375
           VV  +    ++LR G  L K+T +G + SK Q +R+   +  G+ EGA   T   C   A
Sbjct: 311 VVRRLERRMKTLRVGDPLDKNTDVGAINSKAQLQRITELVDAGEAEGATRWT-VPCELPA 369

Query: 376 -GYFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENV 434
            G++ APTVF +V     +A EEIFGPVL+ + + T  E + +AN++ YGL+AG+WTE  
Sbjct: 370 RGFWFAPTVFTDVSQTHRVATEEIFGPVLSVLTFRTPQEAVAKANNTPYGLSAGIWTEKG 429

Query: 435 KQAHYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYALDNY 483
            +  ++AD+L+AG VW N +N FD  SPFGGYK+SG GRE G + L+ Y
Sbjct: 430 SRILWMADQLKAGVVWANTFNRFDPTSPFGGYKESGYGREGGRHGLEAY 478


Lambda     K      H
   0.316    0.133    0.391 

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: 636
Number of extensions: 26
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: 485
Length adjustment: 34
Effective length of query: 461
Effective length of database: 451
Effective search space:   207911
Effective search space used:   207911
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