GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Porphyrobacter dokdonensis DSW-74

Align Probable aldehyde dehydrogenase; EC 1.2.1.3 (uncharacterized)
to candidate WP_068863379.1 I603_RS06550 aldehyde dehydrogenase family protein

Query= curated2:P33008
         (488 letters)



>NCBI__GCF_001677335.1:WP_068863379.1
          Length = 475

 Score =  376 bits (966), Expect = e-109
 Identities = 204/466 (43%), Positives = 288/466 (61%), Gaps = 11/466 (2%)

Query: 29  IGGHGVATSDYLPVLNPATRQPIGQCPVASEEHVEQARAAAGDAFAVWRQVPYGKRCEQL 88
           IGG  +AT  +L V+NPAT Q IGQ P   ++ +++A AAA  AF  W++ P  +R   +
Sbjct: 9   IGGEMIATDRWLDVVNPATEQVIGQVPACGKDELDKAVAAARAAFKTWKKTPIEERRAAI 68

Query: 89  QALAGILEAHLDELAQLLTHEQGKPLADARGELAGAIAFCQCAGSLPLPEVVHEQSATRL 148
            A++G ++ + +EL +LLT EQGKP   A+GE+ GA        +L L + ++E S  RL
Sbjct: 69  MAISGAIKENAEELYRLLTSEQGKPHDQAKGEIYGAAGMSAAQSTLSLDDEINEDSDARL 128

Query: 149 SKTVREPLGVVVAIVPWNYPVSIAFVK--PDRRVGCRKHADSQAGADHAADYLRIGELIR 206
           S+T R P+GVV  IVPWN+PV +A  K  P    GC                LRI ELI 
Sbjct: 129 SRTRRVPVGVVGGIVPWNFPVMMAIQKIVPAMLSGCTIVLKPSPFTPLTT--LRIAELIA 186

Query: 207 DALPAGVINVLAGNDDLGPWLTGHADVAKISFTGSSVTGRHVARSAAADLKRLTLELGGN 266
           D +PAGV+N++ G DDLGP +T H D+ KI+FTGS+ TG+ +   A+ADLKR+TLELGGN
Sbjct: 187 DKVPAGVVNIITGEDDLGPMITSHPDIDKITFTGSTATGKKIMEGASADLKRITLELGGN 246

Query: 267 DAAVVMADSLSDAVVERVFWSAFTNAGQICMATKRLYIHESIYEAFRDKLVAYAQNVVIG 326
           DA++V+ D+    V E++FWS+F+NAGQIC+A KR+YIHE IY+     +V YA+ V +G
Sbjct: 247 DASIVLPDADPKKVAEQLFWSSFSNAGQICVAAKRVYIHEDIYDELSAAIVEYAKTVKVG 306

Query: 327 DGSQPGVTMGPLQNAKQFAKVMSLIDAVRQRGGRLIECGQM-RGGDGYFLPITFVDLPDE 385
           DGSQ G  +GP+QN KQ+ +V+ LI+  +  G + +  G     G GYF+P+T +D P E
Sbjct: 307 DGSQQGTGVGPIQNKKQYDRVLELIEDAKSNGYKFLLGGNADPSGTGYFVPLTILDNPPE 366

Query: 386 SAPEVVEEAFGPLLPLLKFRDVDEVIERVNAARTGWLAASGVVIGRSAHGL---QQPSTR 442
            A  V EE FGP++PL+KF   +EVI R N +  G   A  V       G+   +Q  T 
Sbjct: 367 DARIVAEEQFGPVMPLMKFSSEEEVIARANNSEYG--LAGAVWTANPEKGVEIAEQLETG 424

Query: 443 SVWSTTGCDHAVYS-FGGMKASGYGAESGLEGLLEFTTQKTVIIQQ 487
           +VW       + ++ FGG K SG+GAE G EGL EFT  + + +++
Sbjct: 425 TVWVNEYLHLSPFAPFGGHKQSGFGAEYGKEGLKEFTYPQVITVKK 470


Lambda     K      H
   0.319    0.134    0.398 

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: 590
Number of extensions: 26
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: 488
Length of database: 475
Length adjustment: 34
Effective length of query: 454
Effective length of database: 441
Effective search space:   200214
Effective search space used:   200214
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 (21.7 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