GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_068168204.1 HTA01S_RS06375 betaine-aldehyde dehydrogenase

Query= BRENDA::P05091
         (517 letters)



>NCBI__GCF_001592305.1:WP_068168204.1
          Length = 485

 Score =  362 bits (930), Expect = e-104
 Identities = 202/465 (43%), Positives = 279/465 (60%), Gaps = 11/465 (2%)

Query: 52  KTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADL 111
           + F +VNP+TG     V E  ++DV++AV+AA A F L   W  M A+ RGR+L R AD+
Sbjct: 20  QVFESVNPATGRAYAVVHEATQDDVNRAVEAAGAGFAL---WSAMSATERGRILRRAADI 76

Query: 112 IERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYT 171
           +      LAALE  D GKP   + +VD+     C+ Y+AG A    G+  P+  + F+YT
Sbjct: 77  LRERNHELAALEVRDCGKPIQEALVVDVMSGADCIEYFAGAAATLTGQQYPLK-NAFAYT 135

Query: 172 RHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFP 231
           R EP+GVC  I  WN+P+ +  WK  PALA GN ++ K +E TP TA+ +A +  EAG P
Sbjct: 136 RKEPLGVCVGIGAWNYPIQIACWKSAPALAAGNAMIFKPSELTPATAVKLAEVYLEAGVP 195

Query: 232 PGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIG-RVIQVAAGSSNLKRVTLELGGKS 290
           PGV N+V G G   GA +A+H DV KV+ TGS   G RV++ AAG+  LKRVT+ELGGKS
Sbjct: 196 PGVFNVVQGRG-AVGAMLAAHPDVAKVSVTGSVPTGKRVMETAAGT--LKRVTMELGGKS 252

Query: 291 PNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGN 350
           P ++  DAD++ AV  A    F+ QG+ C   +R FVQ  I   F+ R   R     VG+
Sbjct: 253 PLLVFDDADLEQAVAAAMMGNFYTQGEVCTNCTRVFVQRGIAPRFLARLKERTLLLRVGD 312

Query: 351 PFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGY---FIQPTVFGDVQ 407
           P D  TE G  + E    +++ YI +G+ EGA L+CGG   A  G    F+ PT+F D +
Sbjct: 313 PTDPDTEIGALISEAHTARVMDYIASGQAEGATLVCGGERVAVEGLGDQFVAPTIFADCR 372

Query: 408 DGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGT 467
           D M I +EEIFGPV+ +L F T  E + RAN S + LAA VFT DL + + ++  ++AG 
Sbjct: 373 DDMRIVREEIFGPVLSMLTFDTEAEAIARANQSRFSLAAGVFTTDLQRGHRVAAQIRAGI 432

Query: 468 VWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512
            W+N Y++   + PFGG   SG G E     L  YT++KTV V++
Sbjct: 433 CWINNYNITPIEMPFGGVGESGIGSENSMAALDHYTQLKTVYVEL 477


Lambda     K      H
   0.319    0.136    0.409 

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: 27
Number of successful extensions: 6
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: 517
Length of database: 485
Length adjustment: 34
Effective length of query: 483
Effective length of database: 451
Effective search space:   217833
Effective search space used:   217833
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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