Alignments for a candidate for gatA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Dinoroseobacter shibae DFL-12

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate 3609401 Dshi_2785 glutamyl-tRNA(Gln) amidotransferase, A subunit (RefSeq)

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__Dino:3609401
          Length = 495

 Score =  437 bits (1124), Expect = e-127
 Identities = 239/481 (49%), Positives = 327/481 (67%), Gaps = 18/481 (3%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I   +  +  +EI  ++L +     ++     + AF+    + ARA A    EA D R  
Sbjct: 9   IAAARDKLRAREITATELTEACLAEVEGAG-ALGAFVHNTPDLARAQA----EAADARLA 63

Query: 68  HG---LLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNM 124
            G    + G+P+G+KD   TKG+ +  +S IL  F P Y++TV  +L  A AV +GKLNM
Sbjct: 64  AGDAPAMCGIPLGIKDLFCTKGVPSQAASAILGGFKPEYESTVTSQLFAAGAVMLGKLNM 123

Query: 125 DEFAMGSSTENSAYKLTKNPW---NLDTV--PGGSSGGSAAAVAAGEVPFSLGSDTGGSI 179
           DEFAMGSS E S Y    NPW   N DT   PGGSSGGSA+AVAA     + G+DTGGSI
Sbjct: 124 DEFAMGSSNETSTYGNAVNPWRRGNEDTALTPGGSSGGSASAVAADLCLAATGTDTGGSI 183

Query: 180 RQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDST 239
           RQPA+F G+ GLKPTYGR SR+G+VAFASSLDQ GP+T+ V D A +L A++G D  DST
Sbjct: 184 RQPAAFVGITGLKPTYGRCSRWGIVAFASSLDQAGPMTKDVRDCAIMLGAMAGHDPKDST 243

Query: 240 SANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSL 299
           SA++ VPDF + LTGDI+G  I +PKEY  +G+ +E         ++L   GA   +++L
Sbjct: 244 SADLPVPDFEAMLTGDIRGKVIGIPKEYRMDGMPEEIEALWSRGAEMLRDAGAELRDITL 303

Query: 300 PHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNA--DNLIDLYKQTRAEGFGNEVKR 357
           PH+KYAL  YY+++ +EAS+NLAR+DG+R+G+R   A  D + ++Y++TRAEGFG+EV+R
Sbjct: 304 PHTKYALPAYYVIAPAEASSNLARYDGVRFGHRAKLAQGDGITEMYEKTRAEGFGHEVQR 363

Query: 358 RIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEK-YDVIVGPTTPTPAFKIGENTK 416
           RIM+GT+ LS+G+YDAYY +A+KVR LIK+DF++VF    D I+ P TP+ AF +GE  +
Sbjct: 364 RIMIGTYVLSAGFYDAYYNRARKVRALIKRDFDEVFAAGVDAILTPATPSAAFGLGEMAE 423

Query: 417 -DPLTMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQ 474
            DP+ MY ND+ T+ VNLAG+PGI+VP GL   GLPLGLQ+IG+ ++E  +   A+A EQ
Sbjct: 424 ADPVQMYLNDVFTVTVNLAGLPGIAVPAGLDKQGLPLGLQLIGRPWEEGDLLNTAYALEQ 483

Query: 475 A 475
           A
Sbjct: 484 A 484


Lambda     K      H
   0.315    0.134    0.381 

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: 608
Number of extensions: 31
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: 485
Length of database: 495
Length adjustment: 34
Effective length of query: 451
Effective length of database: 461
Effective search space:   207911
Effective search space used:   207911
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: 52 (24.6 bits)

Align candidate 3609401 Dshi_2785 (glutamyl-tRNA(Gln) amidotransferase, A subunit (RefSeq))
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00132.hmm
# target sequence database:        /tmp/gapView.9767.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00132  [M=466]
Accession:   TIGR00132
Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.1e-163  531.3   0.0   1.2e-163  531.1   0.0    1.0  1  lcl|FitnessBrowser__Dino:3609401  Dshi_2785 glutamyl-tRNA(Gln) ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609401  Dshi_2785 glutamyl-tRNA(Gln) amidotransferase, A subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  531.1   0.0  1.2e-163  1.2e-163       3     463 ..      14     484 ..      12     487 .. 0.96

  Alignments for each domain:
  == domain 1  score: 531.1 bits;  conditional E-value: 1.2e-163
                         TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdiett 77 
                                       ++l ++e++++e++e++l+++e     + af+++t++ a ++a++ d+++a  +   + gip+++Kd +++k+++  
  lcl|FitnessBrowser__Dino:3609401  14 DKLRAREITATELTEACLAEVEGAGA-LGAFVHNTPDLARAQAEAADARLAaGDaPAMCGIPLGIKDLFCTKGVPSQ 89 
                                       678899*****************999.**********************99755359******************** PP

                         TIGR00132  78 caSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....eneervpGGSsgGsaaav 149
                                       +aS iL ++++ y++tV+ +l +aga+++Gk N+DEFamGss etS++g   nP     e+++  pGGSsgGsa av
  lcl|FitnessBrowser__Dino:3609401  90 AASAILGGFKPEYESTVTSQLFAAGAVMLGKLNMDEFAMGSSNETSTYGNAVNPwrrgnEDTALTPGGSSGGSASAV 166
                                       ******************************************************65555567789************ PP

                         TIGR00132 150 aadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDst 226
                                       aadl+  a g+DTGgSiRqPA+f g+ GlKPtYG+ SR+G+va+asSldq G+++k+v d a++l +++g+D kDst
  lcl|FitnessBrowser__Dino:3609401 167 AADLCLAATGTDTGGSIRQPAAFVGITGLKPTYGRCSRWGIVAFASSLDQAGPMTKDVRDCAIMLGAMAGHDPKDST 243
                                       ***************************************************************************** PP

                         TIGR00132 227 slevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiispsE 303
                                       s++ +v+++   l+ d++g  +g+ ke++ +++++e+++ + +  e l++ gae+ ++ lp+ k+al++Yy+i+p+E
  lcl|FitnessBrowser__Dino:3609401 244 SADLPVPDFEAMLTGDIRGKVIGIPKEYRMDGMPEEIEALWSRGAEMLRDAGAELRDITLPHTKYALPAYYVIAPAE 320
                                       ***************************************************************************** PP

                         TIGR00132 304 assnlarydgiryGkrveelks..lkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefek 378
                                       assnlarydg+r+G+r++ ++   ++e+y ktR+egfg+ev+rRim+G+y+ls++ yd+yy++A kvr li+++f++
  lcl|FitnessBrowser__Dino:3609401 321 ASSNLARYDGVRFGHRAKLAQGdgITEMYEKTRAEGFGHEVQRRIMIGTYVLSAGFYDAYYNRARKVRALIKRDFDE 397
                                       ****************98666556***************************************************** PP

                         TIGR00132 379 lf.eevDvivsptaptlafklgekaed.plemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkl 453
                                       +f   vD i++p++p  af lge ae  p++myl+Dv+tv++nlaGlp+i+vP+g +++glp+Glq+ig+ +++  l
  lcl|FitnessBrowser__Dino:3609401 398 VFaAGVDAILTPATPSAAFGLGEMAEAdPVQMYLNDVFTVTVNLAGLPGIAVPAGLDKQGLPLGLQLIGRPWEEGDL 474
                                       **557******************98755************************************************* PP

                         TIGR00132 454 lsvakaleqa 463
                                       l+ a+aleqa
  lcl|FitnessBrowser__Dino:3609401 475 LNTAYALEQA 484
                                       ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (495 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.21
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis