Alignments for a candidate for gatA in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Synechococcus elongatus PCC 7942

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate Synpcc7942_2117 Synpcc7942_2117 aspartyl/glutamyl-tRNA amidotransferase subunit A

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__SynE:Synpcc7942_2117
          Length = 479

 Score =  550 bits (1417), Expect = e-161
 Identities = 278/479 (58%), Positives = 361/479 (75%), Gaps = 4/479 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I EL   + +KE    ++ + + +RI+ ++ ++++FL +  ++A A AK +D+ +    E
Sbjct: 4   IRELHSQLVRKERSAVEIAEAALQRIETLEPQLKSFLHVTADQAIAQAKAVDQRIAAGEE 63

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
             LL G+PIG+KDN+ T+G+ TTC+SKIL+ F P Y++TV QRL +A AV +GK N+DEF
Sbjct: 64  ISLLAGIPIGIKDNLCTRGIPTTCASKILQGFVPPYESTVTQRLAEAGAVAVGKTNLDEF 123

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSSTENSAY+ T NPW+L  VPGGSSGGSAAAVAA E   +LGSDTGGSIRQPA+FCG
Sbjct: 124 AMGSSTENSAYQTTANPWDLTRVPGGSSGGSAAAVAADECVVALGSDTGGSIRQPAAFCG 183

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           VVGLKPTYG VSRYGLVA+ASSLDQIGP +R+VED A LL AI+G D  D+TS  V+VPD
Sbjct: 184 VVGLKPTYGLVSRYGLVAYASSLDQIGPFSRSVEDTAILLGAIAGHDPKDATSLKVEVPD 243

Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALA 307
           +   L   + G+K+ V  E + +     A +++ AAL+VL+GLGA   E+S P   Y L 
Sbjct: 244 YTQFLKPSLAGIKVGVITETVTD---SPAGQAMQAALEVLQGLGAEIREISCPRFAYGLP 300

Query: 308 TYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALS 367
            YY+++ SEASANLAR+DG++YGYR + A+ LID+Y +TRAEGFG+EVKRRIM+GT+ALS
Sbjct: 301 AYYIIAPSEASANLARYDGVKYGYRVEEAETLIDMYCRTRAEGFGSEVKRRIMIGTYALS 360

Query: 368 SGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDIL 427
           +GYYDAYY KAQKVRTLIK+DFE  F + DV+V PTTPT AFK GE T DPL+MY +D++
Sbjct: 361 AGYYDAYYLKAQKVRTLIKQDFEAAFAEVDVLVSPTTPTTAFKAGEKTADPLSMYLSDLM 420

Query: 428 TIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPEL 485
           TIPVNLAG+PG+S+PCG  + GLP GLQIIG    E  V   A+A+EQAT+ H  +P L
Sbjct: 421 TIPVNLAGLPGLSLPCGFDEAGLPYGLQIIGNVLREDQVLHTAYAYEQATEWHLRQPAL 479


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: 616
Number of extensions: 17
Number of successful extensions: 3
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: 479
Length adjustment: 34
Effective length of query: 451
Effective length of database: 445
Effective search space:   200695
Effective search space used:   200695
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 Synpcc7942_2117 Synpcc7942_2117 (aspartyl/glutamyl-tRNA 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.8746.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-204  666.3   0.0   1.3e-204  666.1   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2117  Synpcc7942_2117 aspartyl/glutamy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2117  Synpcc7942_2117 aspartyl/glutamyl-tRNA amidotransferase subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  666.1   0.0  1.3e-204  1.3e-204       2     465 ..       8     471 ..       7     472 .. 0.98

  Alignments for each domain:
  == domain 1  score: 666.1 bits;  conditional E-value: 1.3e-204
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKd 67 
                                               +++l++ke s++e++e+ l+rie+ + ++++fl+vt+++a+++ak++d+++a  +e ++lagipi++Kd
  lcl|FitnessBrowser__SynE:Synpcc7942_2117   8 HSQLVRKERSAVEIAEAALQRIETLEPQLKSFLHVTADQAIAQAKAVDQRIAagEEiSLLAGIPIGIKD 76 
                                               6788999********************************************9976667*********** PP

                                 TIGR00132  68 niavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneer 136
                                               n+++++i+ttcaSkiL+++v+py++tV++rl eaga+ +GktNlDEFamGsste+Sa++ t+nP++ +r
  lcl|FitnessBrowser__SynE:Synpcc7942_2117  77 NLCTRGIPTTCASKILQGFVPPYESTVTQRLAEAGAVAVGKTNLDEFAMGSSTENSAYQTTANPWDLTR 145
                                               ********************************************************************* PP

                                 TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilak 205
                                               vpGGSsgGsaaavaad++++algsDTGgSiRqPA+fcgvvGlKPtYGlvSRyGlvayasSldqiG++++
  lcl|FitnessBrowser__SynE:Synpcc7942_2117 146 VPGGSSGGSAAAVAADECVVALGSDTGGSIRQPAAFCGVVGLKPTYGLVSRYGLVAYASSLDQIGPFSR 214
                                               ********************************************************************* PP

                                 TIGR00132 206 kvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekl 274
                                               +ved+a++l +i+g+D kD tsl+v+v+++++ lk  l g+kvgv+ e   +   +   ++++++le+l
  lcl|FitnessBrowser__SynE:Synpcc7942_2117 215 SVEDTAILLGAIAGHDPKDATSLKVEVPDYTQFLKPSLAGIKVGVITETVTD---SPAGQAMQAALEVL 280
                                               ***********************************************99877...88999********* PP

                                 TIGR00132 275 eelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevk 343
                                               + lgaei e+s+p++ + l++Yyii+psEas+nlarydg++yG+rvee++ l ++y +tR+egfg+evk
  lcl|FitnessBrowser__SynE:Synpcc7942_2117 281 QGLGAEIREISCPRFAYGLPAYYIIAPSEASANLARYDGVKYGYRVEEAETLIDMYCRTRAEGFGSEVK 349
                                               ********************************************************************* PP

                                 TIGR00132 344 rRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsD 412
                                               rRim+G+yals++yyd+yy+kAqkvrtli+++fe +f evDv+vspt+pt+afk gek++dpl+mylsD
  lcl|FitnessBrowser__SynE:Synpcc7942_2117 350 RRIMIGTYALSAGYYDAYYLKAQKVRTLIKQDFEAAFAEVDVLVSPTTPTTAFKAGEKTADPLSMYLSD 418
                                               ********************************************************************* PP

                                 TIGR00132 413 vltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               ++t+p+nlaGlp++s+P+g +e glp Glqiig+++ ++++l+ a+a+eqa++
  lcl|FitnessBrowser__SynE:Synpcc7942_2117 419 LMTIPVNLAGLPGLSLPCGFDEAGLPYGLQIIGNVLREDQVLHTAYAYEQATE 471
                                               **************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (479 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: 00:00:00.02
# Mc/sec: 10.96
//
[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