GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Pseudomonas simiae WCS417

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate GFF3560 PS417_18230 amidase

Query= curated2:Q8THJ1
         (476 letters)



>FitnessBrowser__WCS417:GFF3560
          Length = 504

 Score =  263 bits (673), Expect = 8e-75
 Identities = 162/439 (36%), Positives = 242/439 (55%), Gaps = 37/439 (8%)

Query: 52  KIDVEG-HEGPLAGVPIAIKDNISVVGLPNSCGSKILEGYVPPFNAHVIEKLLDAGAVIL 110
           + +V G  +G LAG  +A+KDNIS+ G+P   G+K LEG+VP F+A V+ +LLDAGA IL
Sbjct: 77  RTEVSGARDGKLAGKTVALKDNISLAGVPMMNGAKPLEGHVPSFDATVVTRLLDAGATIL 136

Query: 111 GKTNLDEFAMGSSTETSYYGPTANPWDLERVPGGSSGGSAAVVAAGEAPFALGSDTGGSV 170
           GK   + + +   + TS   P  NP+      GGSS GSAA+VAAGE   A+G D GGS+
Sbjct: 137 GKATCEHYCLSGGSHTSDPAPVHNPYRHGFASGGSSSGSAALVAAGEVDLAVGGDQGGSI 196

Query: 171 RCPAAFCGVVGLKPTYGAVSRYGVVAYANSLEQVGPLANNVEDIAILMDVIAGYD----R 226
           R P+AFCG  G+KPT+G V   G++A   +++  GP+  NV D A++++V+AG D    R
Sbjct: 197 RIPSAFCGTYGMKPTHGLVPYTGIMAIEATIDHAGPITANVRDNALMLEVMAGADGLDPR 256

Query: 227 RDSTSIDSKTEYQKALVDDVKGLKIGVPKEFFG-EGIHPGVEKAVWNAIHKFESLGATRQ 285
           + +  +D+ ++Y   L   V GLKIGV +E F      P V  +V NAI +F  LGA  +
Sbjct: 257 QAAPQVDTYSDY---LARGVSGLKIGVLREGFELANQDPRVASSVRNAIARFSQLGAQVE 313

Query: 286 EVSMPNINYALASYYIIAMSEASSNLARFDGTRYGFRANGENWHAMVS----------KT 335
           EVS+P    A A ++ I     +  +   +G        G NW  +            + 
Sbjct: 314 EVSVPEHAIAGALWHPIGCEGLTMQMMHGNGA-------GFNWKGLYDVGLLDKQAGWRD 366

Query: 336 RAEGFGTEVKRRILLGTYALSAGYHDKYYLKALKVRTLVKQDFDKALSTVDLLMAPTM-- 393
           +A+     +K  + +G Y +   Y+ ++Y KA  +R L +  +D AL+  DLL+ PT+  
Sbjct: 367 QADDLSASLKLCMFVGQYGVER-YNGRFYAKAQNLRRLARSAYDAALARYDLLVMPTVPI 425

Query: 394 -----PNPAFRIGEKIEDPLTLYLSDVNTCPINLAGVPSVSVPCGFTDGLPVGLQIMGKP 448
                P P   I E +   L +     N    ++ G P++S+PCG  DGLPVGL ++GK 
Sbjct: 426 IAQPHPEPDCSITEYVARALEMI---GNASAQDITGHPAMSIPCGLVDGLPVGLMLVGKH 482

Query: 449 FDEPTVLRAAYTFEKNTDY 467
           + E T+ +AA  FE   D+
Sbjct: 483 YAEGTIYQAAAAFEAAVDW 501


Lambda     K      H
   0.315    0.134    0.391 

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: 583
Number of extensions: 30
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: 476
Length of database: 504
Length adjustment: 34
Effective length of query: 442
Effective length of database: 470
Effective search space:   207740
Effective search space used:   207740
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 (21.5 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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