GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Methanospirillum lacunae Ki8-1

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_109969613.1 DK846_RS14130 acetylornithine transaminase

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_003173355.1:WP_109969613.1
          Length = 384

 Score =  217 bits (552), Expect = 6e-61
 Identities = 130/405 (32%), Positives = 199/405 (49%), Gaps = 51/405 (12%)

Query: 38  IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97
           I+I +G G  V D DG  + D  +G+ V + GH HP+VV+AI +QA +  H S   F+  
Sbjct: 23  IMITKGSGCTVTDADGKQYLDLVAGIAVCSTGHCHPKVVKAIAEQAAELIHCSNL-FYVP 81

Query: 98  NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQA 157
           +   LA+KL+E++      K  + NSGAEA E A+KL +  TGRK+F+A    FHGRT  
Sbjct: 82  HQGALAKKLVEISGLPGNAKAFFSNSGAEAMEGALKLARIRTGRKEFIACEGGFHGRTMG 141

Query: 158 VLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFR 217
            L+ T    +++  F P  P  + +PY                           +    +
Sbjct: 142 SLACTHKPAIREP-FMPLQPFTSFVPYG--------------------------DVQALK 174

Query: 218 HVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWA 277
                E  A+  EPIQGEGG ++PP G+ K +++  D  G+LL  DEVQ G+GRTG ++A
Sbjct: 175 GAITEETAAVILEPIQGEGGVIIPPPGYLKQVREICDAKGVLLIVDEVQSGMGRTGHWFA 234

Query: 278 IEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGRHATTFGGNPVAIAAGIEVVEI 337
            +  G+ PD+I   KA+  G P+  ++ R  + F K   H +TF G P+A AA +  +++
Sbjct: 235 FQEEGIHPDIITMAKAMASGFPMGAIVAREGLEFGK-SEHGSTFAGGPIACAAALASIDV 293

Query: 338 VKELLPHVQEVGDYLHKYLEEFKEKYE--VIGDARGLGLAQAVEIVKSKETKEKYPELRD 395
           + ++LP V   G+     L     + +  +IG   G   A                    
Sbjct: 294 IGKVLPEVAAKGERFRAALAHLNPRVKGLMIGITIGDHCAD------------------- 334

Query: 396 RIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEAL 440
            + KE A  GL++      ++R +PPL +T  EID A  I   A+
Sbjct: 335 -VQKECAVHGLLVNCAAHGNLRLVPPLTITNAEIDKATGIINAAV 378


Lambda     K      H
   0.320    0.141    0.418 

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: 423
Number of extensions: 26
Number of successful extensions: 5
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: 445
Length of database: 384
Length adjustment: 31
Effective length of query: 414
Effective length of database: 353
Effective search space:   146142
Effective search space used:   146142
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 (21.7 bits)
S2: 50 (23.9 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