GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Magnetospirillum magneticum AMB-1

Align 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)
to candidate WP_011384971.1 AMB_RS13035 NAD(P)-dependent oxidoreductase

Query= SwissProt::O18404
         (255 letters)



>NCBI__GCF_000009985.1:WP_011384971.1
          Length = 248

 Score =  117 bits (294), Expect = 2e-31
 Identities = 81/257 (31%), Positives = 135/257 (52%), Gaps = 18/257 (7%)

Query: 3   KNAVSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKEL---GDKVVFVPVDV 59
           ++ V+L+TGGASG+G  T + +A+ GA V++AD+    G + A EL   G K  FV +DV
Sbjct: 4   EDKVALITGGASGIGYCTVKSMAELGADVLIADINVEAGEKAAAELTAKGFKAEFVRLDV 63

Query: 60  TSEKDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVGT 119
           T + +++   +      GRLD+  N AG    ++ F  N +         +V+++N  G 
Sbjct: 64  TDKANIARVKEHVVATRGRLDILCNVAGWGH-IQPFVDNDDAF-----IAKVMSLNLTGP 117

Query: 120 FNVIRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARD 179
             +IR    LM       + + G IVN AS A   G +G++ YSA+K  ++  +  +AR+
Sbjct: 118 IELIRAFFPLM------IEKKTGKIVNVASDAGRVGSLGESVYSAAKGGLIAFSKALARE 171

Query: 180 LSTQGIRICTIAPGLFNTPMLAALPEKVRTFLAKSIPFPQRLGEPSEYAHLVQAIYEN-- 237
            +   I +  I PG  +TP+L + PEK      K IP  +R G+P E A  +  +  N  
Sbjct: 172 GARFNINVNAICPGPTDTPLLKSEPEKFLEAFLKVIPM-RRFGQPQEVADSIVFMASNRA 230

Query: 238 PLLNGEVIRIDGALRMM 254
             + G+V+ ++G + M+
Sbjct: 231 DYITGQVLSVNGGITMV 247


Lambda     K      H
   0.317    0.133    0.369 

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: 156
Number of extensions: 10
Number of successful extensions: 3
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: 255
Length of database: 248
Length adjustment: 24
Effective length of query: 231
Effective length of database: 224
Effective search space:    51744
Effective search space used:    51744
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 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