GapMind for Amino acid biosynthesis

 

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

Align glutamine-tRNA ligase (EC 6.1.1.18); glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate Pf1N1B4_4005 Glutaminyl-tRNA synthetase (EC 6.1.1.18)

Query= BRENDA::P00962
         (554 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4005
          Length = 565

 Score =  695 bits (1793), Expect = 0.0
 Identities = 339/551 (61%), Positives = 420/551 (76%), Gaps = 7/551 (1%)

Query: 6   ARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLR 65
           A P NF+R II  DL SGKHT + TRFPPEPNGYLHIGHAKSIC+NFG+AQ++ G  +LR
Sbjct: 17  AVPVNFLRPIIQADLDSGKHTQIVTRFPPEPNGYLHIGHAKSICVNFGLAQEFGGVTHLR 76

Query: 66  FDDTNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAYVDEL 125
           FDDTNP KED EY+++I++DV+WLGF WSG VRY+S YFDQLH +A+ELI  G AYVD+L
Sbjct: 77  FDDTNPAKEDQEYIDAIESDVKWLGFEWSGEVRYASQYFDQLHDWAVELIKAGKAYVDDL 136

Query: 126 TPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASPFIV 185
           TPEQ +EYRG+LT+PGKNSP+RDRSVEENL LF +M+AG F++G   LRAKIDMASP + 
Sbjct: 137 TPEQAKEYRGSLTEPGKNSPFRDRSVEENLDLFARMKAGEFKDGARVLRAKIDMASPNMN 196

Query: 186 MRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYDWVL 245
           +RDP++YRI+ A HHQTG+KWCIYP YDFTH  SDA+EGITHS+CTLEF+ +R LY+W L
Sbjct: 197 LRDPIMYRIRHAHHHQTGDKWCIYPNYDFTHGQSDAIEGITHSICTLEFESHRPLYEWFL 256

Query: 246 DNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRRGYTAA 305
           +N+ +P  PRQYEFSRLNL YT+ SKRKL  LV +KHV GWDDPRM T+SG RRRGYT  
Sbjct: 257 ENLPVPAKPRQYEFSRLNLNYTITSKRKLKQLVDEKHVHGWDDPRMSTLSGFRRRGYTPK 316

Query: 306 SIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENY-QGEGEMV 364
           SIR FC+ IG  + D  ++   LE  IR+DL+ +APRAM V+ P+K+VI NY +G+ E +
Sbjct: 317 SIRNFCEMIGTNRSDGVVDFGMLEFSIRDDLDHSAPRAMCVLRPLKVVITNYPEGQVENL 376

Query: 365 TMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVIKAERVE 424
            +  HP K +MG R +PF+ E++IDR DF EE  K YKRL    EVRLR +YVI+A+   
Sbjct: 377 ELACHP-KEDMGVRVLPFARELYIDREDFMEEPPKGYKRLEPNGEVRLRGSYVIRADEAI 435

Query: 425 KDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPVEIRLYDRLFSVPNPGA 484
           KDA+GNI  + C+YD +TL K+P +GRKVKGV+HWV AA ++  E+RLYDRLF   NP  
Sbjct: 436 KDADGNIVELRCSYDPETLGKNP-EGRKVKGVVHWVPAAASVECEVRLYDRLFRSANPEK 494

Query: 485 ADD---FLSVINPESLVIKQGF-AEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPVFN 540
           A+D   FL  INP+SL +  G  AEPSL +A     FQFEREGYF  D + S    PVFN
Sbjct: 495 AEDSASFLDNINPDSLQVLTGCRAEPSLGNAQPEDRFQFEREGYFVADIKDSKPGAPVFN 554

Query: 541 RTVGLRDTWAK 551
           RTV LRD+W +
Sbjct: 555 RTVTLRDSWGQ 565


Lambda     K      H
   0.319    0.137    0.416 

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: 1066
Number of extensions: 40
Number of successful extensions: 4
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: 554
Length of database: 565
Length adjustment: 36
Effective length of query: 518
Effective length of database: 529
Effective search space:   274022
Effective search space used:   274022
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: 53 (25.0 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