GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Methanoculleus horonobensis T10

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_067075818.1 MCUHO_RS07130 glutamate-1-semialdehyde 2,1-aminomutase

Query= BRENDA::B1A0U3
         (469 letters)



>NCBI__GCF_001602375.1:WP_067075818.1
          Length = 415

 Score =  118 bits (296), Expect = 3e-31
 Identities = 100/320 (31%), Positives = 149/320 (46%), Gaps = 34/320 (10%)

Query: 50  PLPIVFAHAKGSSVWDPEGNKYIDFLSGYSAVNQGHCHPKILKALHDQADRLTVSSRAFY 109
           P P     A GS +   +G   ID   GY  +  GH HP I +A+  Q ++  +     Y
Sbjct: 27  PYPFYVERAAGSHLATVDGADLIDCCLGYGPLILGHAHPAIREAIERQLEKGWL-----Y 81

Query: 110 NDRFPVFAEYLTALFG----YDMVLPMNTGAEGVETALKLARKWGYEKKKIPNDEALIVS 165
               P+  +    +       DMV  +++G+E    A++LAR  GY  K+       I+ 
Sbjct: 82  GTPTPLELDLAGIITSDHPAVDMVRFVSSGSEATMAAIRLAR--GYTGKQD------IIK 133

Query: 166 CCGCFNGRTLGVISMSCDNEATRG-------FGPLMPGHLKVDFGDAEAIERIFKEKGDR 218
             G F+G    V+  +     T G          L     +V + D EA+E +     D 
Sbjct: 134 VEGGFHGAHDAVLVKAGSGATTLGVPDSAGVLASLTAHTRQVPYNDTEALEALLAGNDD- 192

Query: 219 VAAFILEPIQGEAGVVIPPDGYLKAVRDLCSKYNVLMIADEIQTGLARTGKMLACDWEDV 278
           VAAFILEPI G  G V+P DGYL  VR++ + ++VL+I DE+ TG  R G   A     +
Sbjct: 193 VAAFILEPIMGNVGPVLPDDGYLADVREITAAHDVLLILDEVITGY-RIGIGGAEVLYGI 251

Query: 279 RPDVVILGKALGGGILPVSAVLADKDVMLCIKPG---QHGSTFGGNPLASAVAIAALEVI 335
           +PD+   GK +GGG LP+ A    +++M  + P        TF GNP + A   AAL  +
Sbjct: 252 KPDLATFGKIIGGG-LPIGAFGGRREIMELVAPAGPVYQAGTFSGNPASLAAGYAALRHL 310

Query: 336 KEE----RLTERSTKLGGEL 351
            E     R  + +T+  GE+
Sbjct: 311 HEHPEIYRRLDDATRAIGEV 330


Lambda     K      H
   0.319    0.137    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: 472
Number of extensions: 26
Number of successful extensions: 6
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: 469
Length of database: 415
Length adjustment: 32
Effective length of query: 437
Effective length of database: 383
Effective search space:   167371
Effective search space used:   167371
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: 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