GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Marinobacter guineae M3B

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_099618346.1 CLH62_RS11815 betaine-aldehyde dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_002744735.1:WP_099618346.1
          Length = 489

 Score =  324 bits (831), Expect = 4e-93
 Identities = 181/468 (38%), Positives = 262/468 (55%), Gaps = 10/468 (2%)

Query: 11  LVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKL 70
           L +  GE  PV NPATG  + E+  A      AA+ +A A FAEW   T   R+  LL+ 
Sbjct: 17  LANRTGETFPVINPATGQAIYEVEVADESVQQAAIESARAGFAEWSAMTAIARSRILLRA 76

Query: 71  ADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGH 130
             ++ E     A +E R+ GKP   A   ++    D   FFAG A  + G    + L G 
Sbjct: 77  VALLRERNDELAAVEVRDTGKPWQEAEAVDVVTGADTLEFFAGLAPSIEGNQ--QDLGGD 134

Query: 131 TSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKD 190
               RR+PLG+ A I  WNYPL ++ WK APALA GN ++ KPSE TP+ A+KLAE+  +
Sbjct: 135 FYYTRREPLGICAGIGAWNYPLQISCWKSAPALACGNAMIFKPSEETPMGAVKLAEIFVE 194

Query: 191 I-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGG 249
              PAGV N++ G  + VG  LT HP++  VS TG +ATG+ +++  AS++K   MELGG
Sbjct: 195 AGVPAGVFNVVQGAAE-VGQWLTHHPEIAKVSFTGEVATGKKVMAAAASTLKDVTMELGG 253

Query: 250 KAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEK-LGAAVATLK 308
           K+P+I+FDDAD+E  +       +Y  G+ CT   R++  + +Y   +E+ L      +K
Sbjct: 254 KSPLIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLYPRFMERMLERTRKNIK 313

Query: 309 SGAPDDESTELGPLSSLAH----LERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTL 364
            G P D +T  G L S  H    L+ + K + E     H       E  KG GY+  PT+
Sbjct: 314 PGDPMDTNTNFGALISEKHRDLVLDYIAKGLSEGATLSHGGRAFEPEDSKG-GYFVEPTI 372

Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424
                 D  IV++E+FGPV+SV  F NE++V+  AN++  GLA+ V+T D+ RAHRV  +
Sbjct: 373 FTDCTDDMTIVKEEIFGPVMSVLTFSNEDEVIARANNTDTGLAAGVFTNDIRRAHRVIHQ 432

Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472
           +Q G  W+N++    +EMP GG KLSG G++     +  YT ++ V +
Sbjct: 433 IQAGICWINSYGASPAEMPVGGYKLSGIGRENGRETIAHYTQIKSVYI 480


Lambda     K      H
   0.317    0.134    0.397 

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: 561
Number of extensions: 24
Number of successful extensions: 4
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: 474
Length of database: 489
Length adjustment: 34
Effective length of query: 440
Effective length of database: 455
Effective search space:   200200
Effective search space used:   200200
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 (21.7 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