GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Galbibacter marinus ck-I2-15

Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate WP_008991607.1 I215_RS08785 aldehyde dehydrogenase family protein

Query= SwissProt::Q9DBF1
         (539 letters)



>NCBI__GCF_000300875.1:WP_008991607.1
          Length = 517

 Score =  497 bits (1279), Expect = e-145
 Identities = 260/503 (51%), Positives = 341/503 (67%), Gaps = 7/503 (1%)

Query: 42  LQDLGLREDNEGVYNGS-WGGRGEVITTYCPANNEPIARVRQASLKDYEETIGKAKKAWN 100
           L+ LG+  +N+G   G+ W   GE I    P +   +A+V+ +S +DY + I  A  A+ 
Sbjct: 14  LEILGIAGENKGSSTGTNWFSSGEWIDVVSPVDGNLMAKVQTSSKEDYNKVIETATAAFE 73

Query: 101 IWADIPAPKRGEIVRKIGDAFREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGL 160
            W  +PAP+RGEIVR+  D  R     LG LVS EMGK   EG+GEVQE +D+CD+A GL
Sbjct: 74  KWKKVPAPQRGEIVRQFADKLRANKTALGELVSYEMGKSFQEGLGEVQEMIDICDFAVGL 133

Query: 161 SRMIGGPTLPSERPGHALIEMWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGA 220
           SR + G T+ SERPGH + E W+PLG+VGII+AFNFPVAV+ WN+A+AL+ G+VC+WK +
Sbjct: 134 SRQLHGLTMHSERPGHRMYEQWHPLGIVGIISAFNFPVAVWSWNSALALVCGDVCVWKPS 193

Query: 221 PTTSLVSVAVTKIIAQVLEDNLLPGAICSLVCGGADIGTTMARDERVNLLSFTGSTQVGK 280
             T L +VA  K+++QVL DN LP  I  LV G + +G  +++D R+ L+S TGST++GK
Sbjct: 194 EKTPLTAVACQKLLSQVLSDNSLPEGISCLVTGDSRVGELLSKDTRIPLVSATGSTRMGK 253

Query: 281 EVALMVQERFGKSLLELGGNNAIIAFEDADLSLVVPSVLFAAVGTAGQRCTTVRRLFLHE 340
            VA  V  R GKSLLELGGNNAII   DAD+ + V   +F AVGT GQRCT+ RRL +H+
Sbjct: 254 IVAKAVASRLGKSLLELGGNNAIIVTPDADIKMTVIGAVFGAVGTCGQRCTSTRRLIVHQ 313

Query: 341 SIHNEVVDRLRSAYSQIRVGNPWDPNILYGPLHTKQAVSMFVRAVEEAKKQGGTVVYGGK 400
            ++++V D L  AY Q+++G+P +     GPL    AV M++ A+E+AK+QG  V+    
Sbjct: 314 KVYDQVKDALVEAYGQLKIGDPLNEANHVGPLIDTDAVKMYLDALEKAKEQGAVVLTESG 373

Query: 401 VMD----HPGNYVEPTIVTGLAHDAPIVHQETFAPILYVFKFQ-DEEEVFEWNNEVKQGL 455
            ++      G YV P +V   ++D  IV QETFAPILY+ K+  D E      N V QGL
Sbjct: 374 RLEGNEYQSGCYVRPAVVEA-SNDFNIVQQETFAPILYLIKYDGDLENAIAMQNGVVQGL 432

Query: 456 SSSIFTKDLGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQ 515
           SS+I T +L     +L  +GSDCGI NVNI TSGAEIGGAFGGEK TGGGRESGSDAWK 
Sbjct: 433 SSAIMTNNLREAELFLSNQGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKV 492

Query: 516 YMRRSTCTINYSTSLPLAQGIKF 538
           YMRR T TINY+T++PLAQGIKF
Sbjct: 493 YMRRQTNTINYTTTIPLAQGIKF 515


Lambda     K      H
   0.319    0.137    0.421 

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: 798
Number of extensions: 32
Number of successful extensions: 3
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: 539
Length of database: 517
Length adjustment: 35
Effective length of query: 504
Effective length of database: 482
Effective search space:   242928
Effective search space used:   242928
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