GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Pseudomonas fluorescens FW300-N1B4

Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate Pf1N1B4_24 Glutamyl-tRNA synthetase (EC 6.1.1.17)

Query= metacyc::MONOMER-13959
         (483 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_24
          Length = 437

 Score =  310 bits (794), Expect = 6e-89
 Identities = 165/437 (37%), Positives = 261/437 (59%), Gaps = 20/437 (4%)

Query: 26  LFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLKWLGIDWDESVDVGGEYGPYRQ 85
           LFNY FA+  GG+FI+R+EDTD+ R+    EQ   + L+WLGIDW E  DVGG +GPYRQ
Sbjct: 1   LFNYCFAKQHGGEFILRIEDTDQLRSTRESEQQIFDALRWLGIDWSEGPDVGGPHGPYRQ 60

Query: 86  SERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIARGEMPRYSGKHRDLTQEEQEK 145
           SER DIY+ Y ++L++ G A+ C+CT EEL++ R EQ+ARGE PRY G+   L++EE  +
Sbjct: 61  SERGDIYQKYCQQLVDMGHAFPCFCTAEELDQMRAEQMARGETPRYDGRALLLSKEEVAR 120

Query: 146 FIAEGRKPSIRFRVPEGKVIAFNDIVKGEISFESDGIGDFVIVKKDGTPTYNFAVAIDDY 205
            +A G    IR +VP   V    D+++G++    D +   V++K DG PTY  A  +DD+
Sbjct: 121 RLAAGEPHVIRMKVPTEGVCVVPDMLRGDVEIPWDRMDMQVLMKTDGLPTYFLANVVDDH 180

Query: 206 LMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTLIVNESRKKLSKRDESIIQFIE 265
           LM +THVLRGE+ + + PK I++Y+ FGW+ PQ  +M L+ N  + KLSKR       + 
Sbjct: 181 LMGITHVLRGEEWLPSAPKLILLYEYFGWEQPQLCYMPLLRNPDKSKLSKRKNP--TSVT 238

Query: 266 QYKELGYLPEALFNFIGLLGWSPVGEEELFTKEQFIEIFDVNRLSKSPALFDMHKLKWVN 325
            Y+ +G++PEA+ N++G +GWS   E E F+ ++ ++ FD++R+S    +FD+ KL W+N
Sbjct: 239 FYERMGFMPEAMLNYLGRMGWSMPDEREKFSLQEMVDNFDLSRVSLGGPIFDIEKLSWLN 298

Query: 326 NQYVKKLDLDQVVELTLPHLQKAGKVGTELSAEEQEWVRKLISLYHEQLSYGAEIVELTD 385
            Q+++ L +++        LQK         A   E++ K+      ++   +++  L  
Sbjct: 299 GQWLRDLPVEEFA----ARLQK--------WALNPEYMMKIAPHVQGRVETFSQVAPLAG 346

Query: 386 LFFTDEIEYNQEAKAV----LEEEQVPEVLSTFAAKLEELEEFTPDNIKASIKAVQKETG 441
            FF   +  N +AK      L  +QV +++     KLE L ++  D+I A+I+AV +   
Sbjct: 347 FFFAGGV--NPDAKLFESKKLSGDQVRQLMQLILWKLESLRQWEKDSITATIQAVVESLE 404

Query: 442 HKGKKLFMPIRVAVTGQ 458
            K +     +  A+TG+
Sbjct: 405 LKLRDAMPLMFAAITGR 421


Lambda     K      H
   0.316    0.137    0.394 

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: 554
Number of extensions: 25
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: 483
Length of database: 437
Length adjustment: 33
Effective length of query: 450
Effective length of database: 404
Effective search space:   181800
Effective search space used:   181800
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 (21.6 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