GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Paenisporosarcina indica PN2

Align Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Brassica turgor-responsive/drought-induced gene 26 protein; Btg-26; EC 1.2.1.3 (characterized)
to candidate WP_075618489.1 GY23_RS06905 aldehyde dehydrogenase family protein

Query= SwissProt::Q41247
         (494 letters)



>NCBI__GCF_001939075.1:WP_075618489.1
          Length = 491

 Score =  340 bits (873), Expect = 5e-98
 Identities = 187/469 (39%), Positives = 288/469 (61%), Gaps = 17/469 (3%)

Query: 22  LGNYVGGKW--LGNGPLVSTLNPANNQVLPIAQVVEASLEDYEIGLKACEEAAKTWMQVP 79
           L NY+GGKW   G+   VS  NPAN + L  AQV  ++ ED  + + A +EA K W  VP
Sbjct: 3   LNNYIGGKWQEAGDAKYVSVTNPANGEEL--AQVRLSTQEDVNLAVAAAKEAQKKWALVP 60

Query: 80  APKRGDIVRQIGDALRSKLDYLGRLLSLEMGKILAEGIGEVQEVIDMCDFAVGLSRQLNG 139
           APKR D + ++G  ++ K ++L ++L+ EMGK++ EG GEVQE IDM  +  G  R+L G
Sbjct: 61  APKRADYLYEVGRIMKEKKEHLAQVLTKEMGKVIEEGRGEVQEGIDMAFYMAGEGRRLFG 120

Query: 140 SVIPSERPNHMMLEMWNPLGIVGVITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLI 199
              PSE  +   + +  P+G+VG+IT +NFP A+  W +  A+V GN  +WK A  TP++
Sbjct: 121 ETTPSELADKFAMSVRAPIGVVGLITPWNFPVAIATWKSFPAMVAGNTFLWKPATETPMM 180

Query: 200 TIAMTKLVAEVLEKNHLPGAIFTAMCG-GAEIGEAIAKDTRIPLVSFTGSSKVGLTVQQT 258
              M    A+V E+  +P  +   + G GA++G A+     + ++SFTGS++ G +V + 
Sbjct: 181 AYEM----AKVFEEAGIPDGVANIVFGSGADVGTAMIDHPDVKVISFTGSTETGRSVAER 236

Query: 259 VSARSGKTLLELSGNNAIIVMDDADIQLAARSVLFAAVGTAGQRCTTCRRLLLHESVYDK 318
                 K  LE+ G NA+IVMDDAD+ LA   +L++A GTAGQRCT C R+++H+ V ++
Sbjct: 237 GGRNLKKVSLEMGGKNAVIVMDDADLGLAVEGILWSAFGTAGQRCTACSRVIVHKDVKEE 296

Query: 319 VLEQLLTSYKQVKIGDPLEKGTLLGPLHTPESKKNFEKGIEVIKSQGGKVLTGGKAV-EG 377
           +  +LLTS +Q+ IGD +++   +GP+   ++ +     +E+ K++G  +L GG+ + +G
Sbjct: 297 LESRLLTSMEQLTIGDGMDETVKIGPVINKKALEKIHSYVEIGKNEGATLLVGGEILSDG 356

Query: 378 E---GNFVEPTII-EISSDAAVVKEELFAPVLYALKFKTFEEAVAINNSVPQGLSSSIFT 433
           E   GN+  PT+   +  D+ + +EE+F PV+  ++  + +EA+ +NNSV  GLSSSIF+
Sbjct: 357 ELAKGNYYAPTLFTNVDRDSRIAQEEIFGPVVSLIEVSSLDEAIEVNNSVTFGLSSSIFS 416

Query: 434 RSPDNIFKWIGPMGSDCGIVNVNIPTNGAEIGGAFGGEKATGGG-REAG 481
           R  + +FK       D GIV VN  T GAEI   FGG K TG G R++G
Sbjct: 417 RDVNTVFK--AQRDLDTGIVYVNAGTTGAEIHLPFGGTKGTGNGHRDSG 463


Lambda     K      H
   0.316    0.135    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: 624
Number of extensions: 29
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: 494
Length of database: 491
Length adjustment: 34
Effective length of query: 460
Effective length of database: 457
Effective search space:   210220
Effective search space used:   210220
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