GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Paenisporosarcina indica PN2

Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate WP_075617353.1 GY23_RS01060 aldehyde dehydrogenase

Query= curated2:P39616
         (456 letters)



>NCBI__GCF_001939075.1:WP_075617353.1
          Length = 462

 Score =  436 bits (1122), Expect = e-127
 Identities = 211/455 (46%), Positives = 306/455 (67%), Gaps = 2/455 (0%)

Query: 4   IPSIISKHKAYFAAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDLHKSEQEAYSTE 63
           +  +I++   +F  G TR  E R   LR LKQA++ HE +++ ALY DLHKSE EAY+TE
Sbjct: 8   VEHMITQQHDFFYTGATRSAEFRKQQLRNLKQAIQHHEREILQALYDDLHKSEFEAYATE 67

Query: 64  IGIVLEEISFVMKRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQLALS 123
           IG VL+ I F++K L +W KP+ VKT L  + +KS I+ EPYG+ L++ P+NYP QL + 
Sbjct: 68  IGFVLDSIGFMIKNLDEWMKPEPVKTSLHLMPAKSFIVREPYGSALIVGPFNYPFQLVME 127

Query: 124 PLIGAIAAGNTVVLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQPFDY 183
           PLIGAI  GN  ++KPSE     +AI+ K+I S F  +YV + EG  + ++ L+  PFD 
Sbjct: 128 PLIGAIIGGNCAIVKPSESAVHTAAIIRKIIESTFTPNYVRVVEGEREETSILIHAPFDT 187

Query: 184 IFFTGSVAVGKIVMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTNAGQT 243
           IFFTGSVAVGK+VM+AAA++L PVTLELGGKSP I+   A++ +AAKRI +GKF NAGQT
Sbjct: 188 IFFTGSVAVGKVVMKAAAERLTPVTLELGGKSPAIIDHTANLAVAAKRIAWGKFVNAGQT 247

Query: 244 CIAPDYLFVHEDIKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLNDGIP 303
           C+APDYL V + +K +    + +AI++FYG   + +P YG+I++ + + RL   +     
Sbjct: 248 CVAPDYLLVQQTVKDEFIHLLMQAIQDFYGEDVQASPDYGRIINAKQFDRLRQLIKQEGQ 307

Query: 304 --LTGGQSDPNHHKIAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEVIEKVQSRPKP 361
             + GG  D +   I PTI++ V  +SP M++EIFGP+LP+ +Y  +   I +V+  PKP
Sbjct: 308 HIIAGGNLDADDLYIEPTIIDGVSWNSPSMEDEIFGPLLPVISYDRLETAISQVRKLPKP 367

Query: 362 LALYLFTTNKEIERAVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIGSYHGFDSFNT 421
           L+ YLF+ N +     L  L FGGGC+NDT+ HV + ++PFGGVG SG+ +YHG  SF  
Sbjct: 368 LSAYLFSENDKAIEYFLEQLPFGGGCINDTISHVGSSHMPFGGVGSSGMNAYHGKYSFEA 427

Query: 422 FTHKKSVVKQTNRFDFAFRYPSSKNGLRMIRKILK 456
           FTH KS++K++ +F     +P  KN +++++  L+
Sbjct: 428 FTHAKSILKKSTKFSVNVAFPPYKNKVKLVKSFLR 462


Lambda     K      H
   0.320    0.137    0.401 

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: 19
Number of successful extensions: 2
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: 456
Length of database: 462
Length adjustment: 33
Effective length of query: 423
Effective length of database: 429
Effective search space:   181467
Effective search space used:   181467
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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