GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Thermocrinis albus DSM 14484

Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_012991318.1 THAL_RS01365 aspartate aminotransferase family protein

Query= BRENDA::B1XNF8
         (418 letters)



>NCBI__GCF_000025605.1:WP_012991318.1
          Length = 379

 Score =  323 bits (827), Expect = 7e-93
 Identities = 177/393 (45%), Positives = 257/393 (65%), Gaps = 21/393 (5%)

Query: 23  YVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLH 82
           ++M TY R PV   KG+G  L+D +GK YLD V+GIA   LG+     ++A+  Q +KL 
Sbjct: 2   WLMETYQRLPVRFVKGKGVYLYDEKGKRYLDLVSGIAVNALGYGDRDQVKAICHQAKKLI 61

Query: 83  HISNLYYIPEQGALAQWIVEHSCAD-KVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPV 141
           H+SNL+  P Q  LA+ +VE      +VFFCNSG EANEAAIKLVR+Y     +  ++  
Sbjct: 62  HVSNLFENPWQEKLAKLLVERFWTKGRVFFCNSGTEANEAAIKLVRRYFRLRGE--DRYR 119

Query: 142 ILSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRV 201
           I++ ++SFHGRT  +++AT Q K Q  F+PL +GF Y  +NDI ++E+ ITD      + 
Sbjct: 120 IITFQNSFHGRTFGSMSATAQKKIQTGFEPLLEGFDYAIFNDISSVEKLITD------KT 173

Query: 202 AAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIE 261
           AA+MLE +QGEGGVR  D ++ + ++++C E G+LL+LDEVQ G+GRTGK++ Y++  +E
Sbjct: 174 AAVMLEIVQGEGGVRVADRQFLEDLQKLCRERGLLLLLDEVQTGIGRTGKFYAYQHFQLE 233

Query: 262 PDIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQENL 320
           PDI T AKGL GG+PIGA++ ++  A  F+ G H STFGGNP +CA+AL VVE + +  L
Sbjct: 234 PDIITLAKGLGGGVPIGALLAREEVAKAFDAGSHGSTFGGNPLACASALVVVEKVSE--L 291

Query: 321 LENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLL 380
           L++V   GE     L  L        +VRG GL+  +E++++ +    EVV  A+EKGL+
Sbjct: 292 LDHVREVGEYFMERLAALGR-----GEVRGMGLMLALELESNCK----EVVLKALEKGLV 342

Query: 381 LAPAGPKVLRFVPPLIVSAAEINEAIALLDQTL 413
           +     KVLRFVPPLI+    ++ A+ +L + L
Sbjct: 343 INCTAKKVLRFVPPLILQKRHVDIAVRILRRVL 375


Lambda     K      H
   0.319    0.136    0.406 

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: 415
Number of extensions: 21
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: 418
Length of database: 379
Length adjustment: 31
Effective length of query: 387
Effective length of database: 348
Effective search space:   134676
Effective search space used:   134676
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: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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