GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Escherichia coli BW25113

Align Glutamate--tRNA ligase; EC 6.1.1.17 (characterized, see rationale)
to candidate 16503 b2400 glutamyl-tRNA synthetase (NCBI)

Query= uniprot:A0A0H3C8P5_CAUVN
         (470 letters)



>FitnessBrowser__Keio:16503
          Length = 471

 Score =  353 bits (907), Expect = e-102
 Identities = 190/466 (40%), Positives = 280/466 (60%), Gaps = 15/466 (3%)

Query: 9   VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68
           + TRFAPSPTG+LH+GGARTAL++WL+AR+ GG+F++R+EDTD ERST  A+ AI +G++
Sbjct: 3   IKTRFAPSPTGYLHVGGARTALYSWLFARNHGGEFVLRIEDTDLERSTPEAIEAIMDGMN 62

Query: 69  WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIRSP 128
           WL L+ D+   +Q  R  R+  V+ ++L +G AY+C+ S E LE  RE+  A+G   R  
Sbjct: 63  WLSLEWDEGPYYQTKRFDRYNAVIDQMLEEGTAYKCYCSKERLEALREEQMAKGEKPRYD 122

Query: 129 WRDAPEGDLSA---PHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTYN 185
            R     +  A   P V+RF  P +G  + +D ++GP+ F N ELDDL++ R DG+PTYN
Sbjct: 123 GRCRHSHEHHADDEPCVVRFANPQEGSVVFDDQIRGPIEFSNQELDDLIIRRTDGSPTYN 182

Query: 186 LAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKRH 245
             VVVDD DM +THVIRG+DH+NN  RQ  I +A+   VP +AH+ +I+G DG KLSKRH
Sbjct: 183 FCVVVDDWDMEITHVIRGEDHINNTPRQINILKALKAPVPVYAHVSMINGDDGKKLSKRH 242

Query: 246 GAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPA-----R 300
           GA +V ++ D GY+PE + NYL RLGW HGD E+FT E+ I +F +  V K+ +     +
Sbjct: 243 GAVSVMQYRDDGYLPEALLNYLVRLGWSHGDQEIFTREEMIKYFTLNAVSKSASAFNTDK 302

Query: 301 LDWAKLNHINAQHLRKADDARLTALALAAAETRGEPLPADAAERIARTVPEVKEGAKTIL 360
           L W   ++INA             +     +TR  P  AD  + +        E  KT+ 
Sbjct: 303 LLWLNHHYINALPPEYVATHLQWHIEQENIDTRNGPQLADLVKLLG-------ERCKTLK 355

Query: 361 ELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAE 420
           E+   C +  +       +  +K L     + L+ +RD+LAA  D+ A  +   +++ A+
Sbjct: 356 EMAQSCRYFYEDFAEFDADAAKKHLRPVARQPLEVVRDKLAAITDWTAENVHHAIQATAD 415

Query: 421 SEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466
              VG GK G  LR  +TG  Q+P L+ T+ A+ +  +I R++ AL
Sbjct: 416 ELEVGMGKVGMPLRVAVTGAGQSPALDVTVHAIGKTRSIERINKAL 461


Lambda     K      H
   0.319    0.135    0.405 

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: 661
Number of extensions: 28
Number of successful extensions: 3
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: 470
Length of database: 471
Length adjustment: 33
Effective length of query: 437
Effective length of database: 438
Effective search space:   191406
Effective search space used:   191406
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: 51 (24.3 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