GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Amantichitinum ursilacus IGB-41

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_053937056.1 WG78_RS06780 aspartate aminotransferase family protein

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_001294205.1:WP_053937056.1
          Length = 400

 Score =  204 bits (518), Expect = 5e-57
 Identities = 132/411 (32%), Positives = 203/411 (49%), Gaps = 46/411 (11%)

Query: 38  IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97
           IV  RG G RV+D  G  + DF  G+ V ++GH HP +V A+ +Q  K  H S   F  E
Sbjct: 21  IVPVRGAGSRVWDQAGKEYIDFGGGIAVNSLGHCHPELVAALTEQGNKLWHISNV-FTNE 79

Query: 98  NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV------KYGTGRKQFLAFYHAF 151
            A+ LA+ L+E        +V + NSGAEANEAA+KL       KYG  + + L+  ++F
Sbjct: 80  PALALAKTLVEHT---FAERVFFCNSGAEANEAALKLARRASIEKYGERKNKVLSALNSF 136

Query: 152 HGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFI 211
           HGRT   +S+        DGF P   G+ H  Y +                     L  +
Sbjct: 137 HGRTFFTVSVGGQP-KYSDGFGPKPAGIEHFKYND---------------------LASL 174

Query: 212 EEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGR 271
           E  +       +   +  EPIQGEGG     + F + ++   D++  LL  DEVQ G GR
Sbjct: 175 EALI-----DDDTACVIIEPIQGEGGVTPATQEFLQGVRALCDKFNALLIFDEVQSGNGR 229

Query: 272 TGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD-KPGRHATTFGGNPVAIAA 330
           TG  +A   FGV PD++   K +GGG P+  ++    +      G H TT+GGNP+A A 
Sbjct: 230 TGSLYAYMDFGVVPDILSTAKGLGGGFPIGAMLTTEKVAKHLVAGTHGTTYGGNPLATAV 289

Query: 331 GIEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKE 388
               + I+   E L  V+   + +   L+   +KY V+ + RG+GL   V++      K 
Sbjct: 290 AGTAISIITRPETLSGVKAKSERIRAGLQAIADKYPVVAEIRGMGLLIGVQL------KA 343

Query: 389 KYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEA 439
           +Y      ++  +A+ G+++L  G + +RF P L+++ +EID  +   E+A
Sbjct: 344 EYAGRSRDVLNAAAEEGVLVLAAGPDVVRFAPSLVISDDEIDAGLARVEKA 394


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: 439
Number of extensions: 25
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 445
Length of database: 400
Length adjustment: 32
Effective length of query: 413
Effective length of database: 368
Effective search space:   151984
Effective search space used:   151984
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