GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Pedobacter sp. GW460-11-11-14-LB5

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate CA265_RS19010 CA265_RS19010 aspartyl/glutamyl-tRNA amidotransferase subunit A

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__Pedo557:CA265_RS19010
          Length = 472

 Score =  422 bits (1084), Expect = e-122
 Identities = 227/467 (48%), Positives = 317/467 (67%), Gaps = 5/467 (1%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           + E++ LI +K++ + DL+   +K+I+  ++ + AF  +    A   AK + + ++   +
Sbjct: 7   LKEIQALISQKQLTLPDLLAYYFKQIEN-NEHLNAFNEVFFLSAEVQAKAIQQKIE-EGK 64

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            G L GM IG+KDNI  K    T SSK+LE F   Y +TVVQRL   +A+ IG+LN DEF
Sbjct: 65  QGKLAGMVIGIKDNICYKDHIVTASSKMLEGFVSPYSSTVVQRLLQEDAIIIGRLNCDEF 124

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMG S E S Y + KN  N D VPGGSSGGSA AV A     +LG+DTGGS+RQPA+FCG
Sbjct: 125 AMGGSNETSYYGVAKNAANPDLVPGGSSGGSAVAVQADMCLSALGTDTGGSVRQPAAFCG 184

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
            +GLKPTYGR+SRYG++A+ASS DQ+GPIT +VED A LLQ ++G D  DST + V VPD
Sbjct: 185 QIGLKPTYGRISRYGVIAYASSFDQVGPITSSVEDAALLLQVLAGEDDYDSTVSPVAVPD 244

Query: 248 FLSSLTGDIKGLKIAVPKEYL-GEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYAL 306
           + + L  + K  KIAV KE +  E +  E + ++L +++ L+  G T E VS     Y +
Sbjct: 245 YPAHL-NEHKKQKIAVLKETIESEALDSEIKSAILRSIEQLKADGHTVEYVSFDLLDYLV 303

Query: 307 ATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFAL 366
             YY+L+++EAS+NL+R+DG+ YG+R   A +L +LYK +RAEGFG EVKRRI+LGTF L
Sbjct: 304 PAYYILTTAEASSNLSRYDGVHYGHRNLEAKSLNELYKLSRAEGFGEEVKRRILLGTFVL 363

Query: 367 SSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDI 426
           S+GYYDAYY+KAQ+VR LI++  + +F+ YD+I+ P  PT AFKIG+N +D + MY  DI
Sbjct: 364 SAGYYDAYYQKAQQVRRLIREKMDVLFQDYDLILSPVAPTAAFKIGDNVQDAIVMYMADI 423

Query: 427 LTIPVNLAGVPGISVPCG-LADGLPLGLQIIGKHFDESTVYRVAHAF 472
            T+  +L+G P I++P G   +GLPL +Q   KHF+E  +   + AF
Sbjct: 424 FTVLPSLSGNPAIALPIGNNTEGLPLSIQFTAKHFEEDKLLAFSQAF 470


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: 552
Number of extensions: 23
Number of successful extensions: 2
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: 472
Length adjustment: 34
Effective length of query: 451
Effective length of database: 438
Effective search space:   197538
Effective search space used:   197538
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: 51 (24.3 bits)

Align candidate CA265_RS19010 CA265_RS19010 (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.443.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.9e-174  566.1   0.3   3.3e-174  565.9   0.3    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS19010  CA265_RS19010 aspartyl/glutamyl-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS19010  CA265_RS19010 aspartyl/glutamyl-tRNA amidotransferase subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.9   0.3  3.3e-174  3.3e-174       2     460 ..      11     470 ..      10     472 .] 0.98

  Alignments for each domain:
  == domain 1  score: 565.9 bits;  conditional E-value: 3.3e-174
                                  TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..kekklagipiavKd 67 
                                                ++l+ +k++++ ++l  + ++ie++++ +naf ev   +a  +ak++++k++  k+ klag++i++Kd
  lcl|FitnessBrowser__Pedo557:CA265_RS19010  11 QALISQKQLTLPDLLAYYFKQIENNEH-LNAFNEVFFLSAEVQAKAIQQKIEegKQGKLAGMVIGIKD 77 
                                                78899******************9998.***********************964446*********** PP

                                  TIGR00132  68 niavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPenee 135
                                                ni+ kd  +t++Sk+Le++vspy++tVv+rl +++a+iiG+ N DEFamG+s etS++gv kn +n +
  lcl|FitnessBrowser__Pedo557:CA265_RS19010  78 NICYKDHIVTASSKMLEGFVSPYSSTVVQRLLQEDAIIIGRLNCDEFAMGGSNETSYYGVAKNAANPD 145
                                                ******************************************************************** PP

                                  TIGR00132 136 rvpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGil 203
                                                 vpGGSsgGsa av ad++  alg+DTGgS+RqPA+fcg +GlKPtYG++SRyG++ayasS+dq+G++
  lcl|FitnessBrowser__Pedo557:CA265_RS19010 146 LVPGGSSGGSAVAVQADMCLSALGTDTGGSVRQPAAFCGQIGLKPTYGRISRYGVIAYASSFDQVGPI 213
                                                ******************************************************************** PP

                                  TIGR00132 204 akkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelse.esldkevkekfekl 270
                                                + +ved+al+l+v++g D  Dst   v+v+++  +l++ +k+ k++v+ke +e e ld+e+k+++ + 
  lcl|FitnessBrowser__Pedo557:CA265_RS19010 214 TSSVEDAALLLQVLAGEDDYDSTVSPVAVPDYPAHLNE-HKKQKIAVLKETIEsEALDSEIKSAILRS 280
                                                **************************************.999********8772568*********** PP

                                  TIGR00132 271 lekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegf 338
                                                +e+l++ g++++ vs++ +++ +++Yyi++++Eassnl+rydg+ yG+r  e+ksl+ely+ +R+egf
  lcl|FitnessBrowser__Pedo557:CA265_RS19010 281 IEQLKADGHTVEYVSFDLLDYLVPAYYILTTAEASSNLSRYDGVHYGHRNLEAKSLNELYKLSRAEGF 348
                                                ******************************************************************** PP

                                  TIGR00132 339 geevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedpl 406
                                                geevkrRi+lG+++ls++yyd+yy+kAq+vr+li+++++ lf+++D+i+sp+apt afk+g++ +d++
  lcl|FitnessBrowser__Pedo557:CA265_RS19010 349 GEEVKRRILLGTFVLSAGYYDAYYQKAQQVRRLIREKMDVLFQDYDLILSPVAPTAAFKIGDNVQDAI 416
                                                ******************************************************************** PP

                                  TIGR00132 407 emylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakal 460
                                                 my++D++tv  +l+G+pai++P+g++++glp+ +q+++k+f+++kll +++a+
  lcl|FitnessBrowser__Pedo557:CA265_RS19010 417 VMYMADIFTVLPSLSGNPAIALPIGNNTEGLPLSIQFTAKHFEEDKLLAFSQAF 470
                                                **************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (472 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.00
//
[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