Alignments for a candidate for gatA in Phaeobacter inhibens BS107

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.1087907.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  FitnessBrowser__Phaeo:GFF2165  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Phaeo:GFF2165  
   #    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.kklagipiavKdniavkdiettcaS 80 
                                    ++l k e++++e++e++l++i+a +  +naf++ t+e al++ k+ d++++  +   + g+pi++Kd +++k++   +aS
  FitnessBrowser__Phaeo:GFF2165  14 DALRKGETTSVELTEACLKAIDAADA-LNAFVHKTPEIALERSKAADARIKaGDaPAMCGLPIGIKDLFCTKGVASQAAS 92 
                                    67889999**************9998.***********************9755359*********************** PP

                      TIGR00132  81 kiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....eneervpGGSsgGsaaavaadlvp 155
                                     iLe++++ y++tV ++l++aga+++Gk N+DEFamGss etS++g    P        e  pGGSsgGsa avaadl+ 
  FitnessBrowser__Phaeo:GFF2165  93 GILEGFKPEYESTVSQQLQDAGAVMLGKLNMDEFAMGSSNETSVYGNAVSPwrrgnDTAELTPGGSSGGSASAVAADLCL 172
                                    ***************************************************33332234789****************** PP

                      TIGR00132 156 lalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDstslevkveel 235
                                     a g+DTGgSiRqPA+f+g+ G+KPtYG+ SR+G+va+asSldq G+++k+v d+a++l++++g+D kDsts++ +v+++
  FitnessBrowser__Phaeo:GFF2165 173 AATGTDTGGSIRQPAAFTGITGIKPTYGRCSRWGVVAFASSLDQAGPMTKSVRDAAMMLEAMCGHDPKDSTSADLAVPNF 252
                                    ******************************************************************************** PP

                      TIGR00132 236 leelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiispsEassnlarydgir 315
                                       l+ d+kg k+g+ +e++ ++++ e+++ + +  e l++ gaeiv++slp+ k+al++Yy+i+p+Eassnlarydg+r
  FitnessBrowser__Phaeo:GFF2165 253 EAMLTGDIKGKKIGIPREYRMDGMPAEIEKLWSEGAEMLRAAGAEIVDISLPHTKYALPAYYVIAPAEASSNLARYDGVR 332
                                    ******************************************************************************** PP

                      TIGR00132 316 yGkrve.elks.lkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklf.eevDvivsptap 392
                                    yG+r++ e+ + ++e+y ktR++gfg+ev+rR+m+G+y+ls++ yd+yy++A kvrtli+++fe++f + +D i++p++p
  FitnessBrowser__Phaeo:GFF2165 333 YGQRATlEAGDgITEMYEKTRAAGFGHEVQRRVMVGTYVLSAGFYDAYYNRARKVRTLIKKDFEDVFaQGIDAILTPATP 412
                                    ****86233336*******************************************************5579********* PP

                      TIGR00132 393 tlafklgekaed.plemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                      af lge  +  p++myl+Dv+tv++nlaGlp+isvP+g + +glp+Glq+ig+ +++  ll+ a+ale+a
  FitnessBrowser__Phaeo:GFF2165 413 SAAFGLGEMIDAdPVQMYLNDVFTVTVNLAGLPGISVPAGIDAQGLPLGLQLIGRPWEEGDLLNTAYALEEA 484
                                    ********98755********************************************************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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 31.28
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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