GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Phaeobacter inhibens BS107

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate GFF2165 PGA1_c21970 glutamyl-tRNA(Gln) amidotransferase subunit A

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__Phaeo:GFF2165
          Length = 495

 Score =  452 bits (1164), Expect = e-132
 Identities = 243/481 (50%), Positives = 332/481 (69%), Gaps = 18/481 (3%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           +++ +  + K E    +L +   K I A D  + AF+    E     A E  +A D R +
Sbjct: 9   LSDARDALRKGETTSVELTEACLKAIDAAD-ALNAFVHKTPE----IALERSKAADARIK 63

Query: 68  HG---LLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNM 124
            G    + G+PIG+KD   TKG+ +  +S ILE F P Y++TV Q+LQDA AV +GKLNM
Sbjct: 64  AGDAPAMCGLPIGIKDLFCTKGVASQAASGILEGFKPEYESTVSQQLQDAGAVMLGKLNM 123

Query: 125 DEFAMGSSTENSAYKLTKNPWN-----LDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSI 179
           DEFAMGSS E S Y    +PW       +  PGGSSGGSA+AVAA     + G+DTGGSI
Sbjct: 124 DEFAMGSSNETSVYGNAVSPWRRGNDTAELTPGGSSGGSASAVAADLCLAATGTDTGGSI 183

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

Query: 240 SANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSL 299
           SA++ VP+F + LTGDIKG KI +P+EY  +G+  E  +      ++L   GA   ++SL
Sbjct: 244 SADLAVPNFEAMLTGDIKGKKIGIPREYRMDGMPAEIEKLWSEGAEMLRAAGAEIVDISL 303

Query: 300 PHSKYALATYYLLSSSEASANLARFDGIRYGYRT--DNADNLIDLYKQTRAEGFGNEVKR 357
           PH+KYAL  YY+++ +EAS+NLAR+DG+RYG R   +  D + ++Y++TRA GFG+EV+R
Sbjct: 304 PHTKYALPAYYVIAPAEASSNLARYDGVRYGQRATLEAGDGITEMYEKTRAAGFGHEVQR 363

Query: 358 RIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVF-EKYDVIVGPTTPTPAFKIGEN-T 415
           R+M+GT+ LS+G+YDAYY +A+KVRTLIKKDFEDVF +  D I+ P TP+ AF +GE   
Sbjct: 364 RVMVGTYVLSAGFYDAYYNRARKVRTLIKKDFEDVFAQGIDAILTPATPSAAFGLGEMID 423

Query: 416 KDPLTMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQ 474
            DP+ MY ND+ T+ VNLAG+PGISVP G+ A GLPLGLQ+IG+ ++E  +   A+A E+
Sbjct: 424 ADPVQMYLNDVFTVTVNLAGLPGISVPAGIDAQGLPLGLQLIGRPWEEGDLLNTAYALEE 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: 583
Number of extensions: 25
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 GFF2165 PGA1_c21970 (glutamyl-tRNA(Gln) amidotransferase subunit A)
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.29938.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   7.8e-168  544.9   0.0   8.9e-168  544.7   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2165  PGA1_c21970 glutamyl-tRNA(Gln) a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2165  PGA1_c21970 glutamyl-tRNA(Gln) amidotransferase subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  544.7   0.0  8.9e-168  8.9e-168       3     463 ..      14     484 ..      12     487 .. 0.95

  Alignments for each domain:
  == domain 1  score: 544.7 bits;  conditional E-value: 8.9e-168
                          TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdiet 76 
                                        ++l k e++++e++e++l++i+a +  +naf++ t+e al++ k+ d++++  +   + g+pi++Kd +++k++  
  lcl|FitnessBrowser__Phaeo:GFF2165  14 DALRKGETTSVELTEACLKAIDAADA-LNAFVHKTPEIALERSKAADARIKaGDaPAMCGLPIGIKDLFCTKGVAS 88 
                                        67889999**************9998.***********************9755359******************* PP

                          TIGR00132  77 tcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....eneervpGGSsgGsaa 147
                                         +aS iLe++++ y++tV ++l++aga+++Gk N+DEFamGss etS++g    P        e  pGGSsgGsa 
  lcl|FitnessBrowser__Phaeo:GFF2165  89 QAASGILEGFKPEYESTVSQQLQDAGAVMLGKLNMDEFAMGSSNETSVYGNAVSPwrrgnDTAELTPGGSSGGSAS 164
                                        *******************************************************33332234789********** PP

                          TIGR00132 148 avaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkk 223
                                        avaadl+  a g+DTGgSiRqPA+f+g+ G+KPtYG+ SR+G+va+asSldq G+++k+v d+a++l++++g+D k
  lcl|FitnessBrowser__Phaeo:GFF2165 165 AVAADLCLAATGTDTGGSIRQPAAFTGITGIKPTYGRCSRWGVVAFASSLDQAGPMTKSVRDAAMMLEAMCGHDPK 240
                                        **************************************************************************** PP

                          TIGR00132 224 DstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyii 299
                                        Dsts++ +v+++   l+ d+kg k+g+ +e++ ++++ e+++ + +  e l++ gaeiv++slp+ k+al++Yy+i
  lcl|FitnessBrowser__Phaeo:GFF2165 241 DSTSADLAVPNFEAMLTGDIKGKKIGIPREYRMDGMPAEIEKLWSEGAEMLRAAGAEIVDISLPHTKYALPAYYVI 316
                                        **************************************************************************** PP

                          TIGR00132 300 spsEassnlarydgiryGkrve.elks.lkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtlii 373
                                        +p+Eassnlarydg+ryG+r++ e+ + ++e+y ktR++gfg+ev+rR+m+G+y+ls++ yd+yy++A kvrtli+
  lcl|FitnessBrowser__Phaeo:GFF2165 317 APAEASSNLARYDGVRYGQRATlEAGDgITEMYEKTRAAGFGHEVQRRVMVGTYVLSAGFYDAYYNRARKVRTLIK 392
                                        ********************86233336************************************************ PP

                          TIGR00132 374 defeklf.eevDvivsptaptlafklgekaed.plemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigka 447
                                        ++fe++f + +D i++p++p  af lge  +  p++myl+Dv+tv++nlaGlp+isvP+g + +glp+Glq+ig+ 
  lcl|FitnessBrowser__Phaeo:GFF2165 393 KDFEDVFaQGIDAILTPATPSAAFGLGEMIDAdPVQMYLNDVFTVTVNLAGLPGISVPAGIDAQGLPLGLQLIGRP 468
                                        *******5579*****************98755******************************************* PP

                          TIGR00132 448 fddkkllsvakaleqa 463
                                        +++  ll+ a+ale+a
  lcl|FitnessBrowser__Phaeo:GFF2165 469 WEEGDLLNTAYALEEA 484
                                        *************987 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.55
//
[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:

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