GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Herbaspirillum seropedicae SmR1

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate HSERO_RS02850 HSERO_RS02850 glutamyl-tRNA(Gln) amidotransferase

Query= curated2:Q9RTA9
         (482 letters)



>FitnessBrowser__HerbieS:HSERO_RS02850
          Length = 651

 Score =  219 bits (559), Expect = 2e-61
 Identities = 169/473 (35%), Positives = 239/473 (50%), Gaps = 33/473 (6%)

Query: 10  LARAVQSGETTPQQLLHGALARAEAVR----GLNALVSLNSHAEEQAAAV-QGRMQAGET 64
           L  A  +G  T + L+   LAR  A       LNA+V+LN  A E+A  + + R Q+G  
Sbjct: 57  LQSAQDAGRATSRSLVLAYLARIRAYDQQGPSLNAIVTLNPKALEEADQLDRERRQSGPR 116

Query: 65  LPLAGVPIVVKDNINVTGTRTTCGSRMLANYVSPYTATAAQKLQGAGAVIVGKANMDEFA 124
            PL G+PI+VKDN +     TT G+  LA   +   A   ++L+ AGAVI+GK  M E A
Sbjct: 117 GPLHGIPILVKDNYDTVDMPTTGGTLALATLQAQADAFQVKRLREAGAVILGKTTMHELA 176

Query: 125 MGSSTESSASGPTLNPWDHERVPGGSSGGSAVAVAAGISPVSLGSDTGGSVRQPAALCGV 184
            G +T SS +G T NP+D  R PGGSSGG+  AVAA  +   +GSDT GS+R PAA   +
Sbjct: 177 AGVTTVSSLTGFTRNPYDPRRAPGGSSGGTGAAVAASFAAAGMGSDTCGSIRIPAAHQNL 236

Query: 185 YGFKPTYGRVSRYGLVAYASSLDQIGPFARSAEDLALLMNVIAGHDPRDATSLDA----P 240
           +G + T G  SR G++  +S+ D   P ARS EDLA++++   G DP+D++++DA    P
Sbjct: 237 FGLRTTRGLASRSGVMPLSSTQDVAAPLARSVEDLAIMLDATVGSDPQDSSTVDANGHIP 296

Query: 241 ARFAVG-GADSLRGLRVGVIRESLGG--NTPGVEAALGATLDALRGAGAVVGEVSIPELE 297
             +  G  ADSL+G R+GV+R   G       V AA+   L  L+  GA+V +V+IPEL+
Sbjct: 297 KSYRDGLRADSLQGARIGVLRALFGAAPEDAEVSAAINKALQQLKDQGAIVTDVTIPELD 356

Query: 298 YAIAAYYLIAMPEASSNLARYDGMVYGERVPGGDVTRSMTLTREQGFGQEVQRR--ILLG 355
             ++   +I          +YD   Y +  PG  V  S+     +G   E+      L  
Sbjct: 357 GLLSGSSIIPYE------FKYDLGAYLQSHPGAPV-GSLGEILARGMEHELLEAGLRLRN 409

Query: 356 TYALSSGYYDAYYAKAMKVRRLIADEFTTAF--GQYDVLVTPTSPFPAFRRGEKASDPLA 413
           +  L +        K M  R  +    T        D LV PT    A   GE     + 
Sbjct: 410 SVDLQNPKDKEELEKVMLKRSALKSLMTDVMQKNHLDTLVYPTIQRKAALIGEPQGGAMN 469

Query: 414 MYAADVDTVAVNLAGLPALSVPAGFEEVDGKRLPVGVQFIAPALQDERLLALA 466
              +          GLPAL++P GF E DG  LPV ++ +AP   +  LL LA
Sbjct: 470 CQLSAT-------TGLPALALPVGFTE-DG--LPVSLELLAPEFAEPALLGLA 512


Lambda     K      H
   0.316    0.132    0.372 

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: 691
Number of extensions: 42
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: 482
Length of database: 651
Length adjustment: 36
Effective length of query: 446
Effective length of database: 615
Effective search space:   274290
Effective search space used:   274290
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: 53 (25.0 bits)

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

Links

Downloads

Related tools

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