GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Marivita geojedonensis DPG-138

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase

Query= BRENDA::P05091
         (517 letters)



>NCBI__GCF_002115805.1:WP_085640679.1
          Length = 485

 Score =  371 bits (953), Expect = e-107
 Identities = 203/473 (42%), Positives = 286/473 (60%), Gaps = 6/473 (1%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           FI+  + +  +    P + P+TGE I  V       VDKA+ AA  A +    W  M  +
Sbjct: 12  FIDGAYVEDTTGTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKA---WAAMSGT 68

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
            RGR+L R AD++      L+ LET D GKPY  +  VD       L Y+ G A    G+
Sbjct: 69  ERGRILRRAADMMRERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAGSLTGE 128

Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219
            I + G+ + YTR EP+GVC  I  WN+P  +  WK  PALA GN +V K +E TPL AL
Sbjct: 129 HIQL-GEDWVYTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCAL 187

Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279
            VA ++ EAG P G+ N+V G G   GA++ +   V KV+ TGS   G+ +  AA +  +
Sbjct: 188 KVAEILHEAGLPAGIYNVVQGLGEV-GASLVTDPRVAKVSLTGSVPTGKKVYAAA-AEQM 245

Query: 280 KRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERS 339
           K VT+ELGGKSP +I  DAD++ AV  A    F++ GQ C  G+R FVQ+ I + F++R 
Sbjct: 246 KHVTMELGGKSPLLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKRL 305

Query: 340 VARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQ 399
             R  + VVG+P D  T  GP V E Q K +L YI  G+ EGA+L+ GG      G+++Q
Sbjct: 306 TERLSTAVVGDPLDEATNFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLNRDGFYLQ 365

Query: 400 PTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYL 459
           PTVF DV+D M IA+EEIFGPVM +L F+T EE + RAN++ +GL+A VFT+DL +A+ +
Sbjct: 366 PTVFADVKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHRV 425

Query: 460 SQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512
              L+AG+ ++N Y+    ++PFGG KMSG GRE  +  +  Y+E+K+V V++
Sbjct: 426 IAQLEAGSCFINSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEMKSVYVRM 478


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: 618
Number of extensions: 30
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: 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 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