GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Sphingomonas indica Dd16

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_085218595.1 B9N75_RS09590 aldehyde dehydrogenase family protein

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_900177405.1:WP_085218595.1
          Length = 479

 Score =  216 bits (550), Expect = 1e-60
 Identities = 150/467 (32%), Positives = 234/467 (50%), Gaps = 19/467 (4%)

Query: 18  KQP-----VYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLAD 72
           KQP     V +  TG V   +A+A A+ +DA + AA  A     +     R   L    D
Sbjct: 17  KQPNADLEVTDKYTGKVAFRVAQADAKTIDAGIAAAVKAAEPMARMASYERQAVLQHCVD 76

Query: 73  VIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG----LAAGEYLE 128
              E     A       GKP++ A   E+  ++D FR  A  +  + G    L   +   
Sbjct: 77  RFTERFDELAYALCVEAGKPINDA-EGEVTRLIDTFRIAAEESVRMTGEVQPLDISKRAR 135

Query: 129 GHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAE-L 187
           G+  + +R P+G  + I+P+N+PL +AA K+APA+A G   V+KP+  TPL A+ + E L
Sbjct: 136 GYMGIWKRVPIGPCSFISPFNFPLNLAAHKIAPAIAVGCPFVMKPASRTPLGAIIMGEVL 195

Query: 188 AKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMEL 247
           A+   P G  +IL    +   D  T   +++++S TGS   G  + +      K+  +EL
Sbjct: 196 AETDLPKGAFSILPAH-REGADMFTEDERLKLLSFTGSPGVGWDLKAKAGK--KKVVLEL 252

Query: 248 GGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATL 307
           GG A VIV  DAD+E  V  +    +Y +GQ C    RI     IYD L EKL A   TL
Sbjct: 253 GGNAAVIVDKDADLEDAVARIIFGAFYQSGQSCIGVQRIIIHADIYDALKEKLAAKTKTL 312

Query: 308 KSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAG 367
            +G P D  T +GP+  L    R+   ++EA   G  K++ GG   K +G     TLL G
Sbjct: 313 VAGDPHDRKTFVGPMIDLKEATRLDNWIQEA-VEGGAKLLVGG---KRDGAMLEATLLEG 368

Query: 368 ALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQY 427
             +   + ++E FGPV  ++ FD+    ++  NDS++GL + ++T+D+ +      RL  
Sbjct: 369 VDRSATVYREEAFGPVAILSKFDDFAAALDEVNDSKFGLQAGIFTRDIFQVLNAWDRLDV 428

Query: 428 GCTWVN-THFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473
           G   +N      V  MP+GG K SG G++   + +ED T +R+++++
Sbjct: 429 GGVVINDVPSYRVDNMPYGGVKDSGLGREGIRFAMEDMTEIRNLVIR 475


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: 484
Number of extensions: 22
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: 479
Length adjustment: 33
Effective length of query: 441
Effective length of database: 446
Effective search space:   196686
Effective search space used:   196686
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: 51 (24.3 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