GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Sulfurimonas denitrificans DSM 1251

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein

Query= BRENDA::V4GH04
         (496 letters)



>NCBI__GCF_000012965.1:WP_011373513.1
          Length = 471

 Score =  223 bits (569), Expect = 9e-63
 Identities = 160/469 (34%), Positives = 248/469 (52%), Gaps = 19/469 (4%)

Query: 29  GKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPPSARERILLRLADL 88
           GK +N YN   G++ +E    + +D   A+    A L S    +   + R   LL +A  
Sbjct: 18  GKRVNPYN---GEVASEFVTCNADDAKKALN--IALLASKEASKTTIAQRCSWLLDVASK 72

Query: 89  LEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATKLTGSTLDLSLPLPPEV 148
           L  + +++A+  T   GK + YS++ EV    + +   A     + G T++         
Sbjct: 73  LAQNKEDIAKTITDEVGKPITYSRI-EVERCIETVTLAAETMRTMHGETVNTDA-FASGK 130

Query: 149 RSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAEETPLTALRLAELA 208
           ++ +   RVP GVV AI P+NFPL +   KIAPAL  GN V+LKP  E PLTA + A+L 
Sbjct: 131 KTISFFSRVPCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLF 190

Query: 209 MEAGLPA-GALNVVTGRGETAGDALVRH-PKVAKVAFTGSTEVGRIIGSACGRSLKAVSL 266
           +E+      AL+VV G  +  G  +    P+V  ++FTGS  VG II  + G  +K VSL
Sbjct: 191 IESEFAIKDALSVVYGDADVGGTLVTSEIPRV--ISFTGSVGVGEIITKSAG--IKKVSL 246

Query: 267 ELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYEDVIQRLAVIGE 326
           ELGG +   +    +   AA+  A   F N GQVC +  R+YVH+ IY +   ++A   +
Sbjct: 247 ELGGNAATFIDKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATK 306

Query: 327 SIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPCAQGFFVKPTIF 386
            +VVGS  E+   MGP+V+ +  +  +  +++ I++GA  I      P  +G    P + 
Sbjct: 307 KLVVGSPYEEDTFMGPLVNDEAAKRAMEWVQSAIKEGATPIL----EPRVEGRVFYPCVM 362

Query: 387 ANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWTNDLSAALRINDE 446
           A+  K+D+ ++ QEVF P++      D  E +   N S YGL  SI+TNDL+   R  +E
Sbjct: 363 AD-VKEDMAIVCQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINE 421

Query: 447 LEAGTVWVNTHNMVDPNL-PFGGFKDSGVGREHGAAAIEHYTTTRSLVI 494
           L+AG + +N    +  ++ P+GG K SGVGRE    AIE  +  +S++I
Sbjct: 422 LDAGGIVINDMPTLRFDIQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470


Lambda     K      H
   0.317    0.134    0.395 

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: 518
Number of extensions: 23
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: 496
Length of database: 471
Length adjustment: 34
Effective length of query: 462
Effective length of database: 437
Effective search space:   201894
Effective search space used:   201894
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 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