GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Sphingomonas koreensis DSMZ 15582

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate Ga0059261_0082 Ga0059261_0082 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A (EC 6.3.5.-)

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__Korea:Ga0059261_0082
          Length = 494

 Score =  438 bits (1127), Expect = e-127
 Identities = 233/485 (48%), Positives = 324/485 (66%), Gaps = 10/485 (2%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           +  ++  +   E    ++ D    ++ A   ++ AF+    + A A A+  D A      
Sbjct: 9   VAAIRDGVRSGEFTAIEVADAFITKVSAAK-QLNAFIVETPDHAIAAARTADAARAAGET 67

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
              L G+PIG+KD   TKG++TT +S +LE F P+Y++TV Q+L DA A  +GKLN+D+F
Sbjct: 68  LKPLAGVPIGMKDLFCTKGVQTTAASHMLEGFTPVYESTVSQKLWDAGAGMLGKLNLDQF 127

Query: 128 AMGSSTENSAYKLTKNPW------NLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQ 181
           AMGSS E S +    +PW      N    PGGSSGGS++A+AA  VP + G+DTGGSIRQ
Sbjct: 128 AMGSSNETSYFGNVISPWRRKDGGNAALAPGGSSGGSSSAIAARLVPAATGTDTGGSIRQ 187

Query: 182 PASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSA 241
           PA+F G+ G+KPTYGR SR+G+VAFASSLDQ GP+ R V D A +L+A++G D  D+TS 
Sbjct: 188 PAAFTGISGIKPTYGRCSRWGVVAFASSLDQAGPMARDVRDCAIMLEAMAGFDPKDATSL 247

Query: 242 NVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPH 301
           ++ VP++ + L+ D++G K+ +PKEY  +G+  E        +  L+  GA   EVSLPH
Sbjct: 248 DMAVPNWEAGLSADLRGKKVGIPKEYRVDGMPAEIEALWQQGIDWLKDAGAEIVEVSLPH 307

Query: 302 SKYALATYYLLSSSEASANLARFDGIRYGYR-TDNADNLIDLYKQTRAEGFGNEVKRRIM 360
           +KYAL  YY+++ +EAS+NLAR+DG+RYG R   +  NL ++Y  TRA GFG EV+RRI+
Sbjct: 308 TKYALPAYYIIAPAEASSNLARYDGVRYGQRDLPDGANLQEMYAATRAAGFGPEVQRRIL 367

Query: 361 LGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLT 420
           +GT+ LS+G+YDAYY +AQKVRTLI +DFE  + + D+++ PT P+ AF +GE + DPL 
Sbjct: 368 IGTYVLSAGFYDAYYTQAQKVRTLIAQDFEKAWAQCDLLLTPTAPSAAFALGEKSADPLA 427

Query: 421 MYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHH 479
           MY ND+ T+P +LAG+P +SVP GL  DGLPLGLQIIGK FDE  V   + A EQ     
Sbjct: 428 MYLNDVFTVPSSLAGIPAMSVPGGLDKDGLPLGLQIIGKPFDEQGVLNASLAIEQRAG-F 486

Query: 480 KAKPE 484
            AKPE
Sbjct: 487 TAKPE 491


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: 573
Number of extensions: 18
Number of successful extensions: 4
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: 494
Length adjustment: 34
Effective length of query: 451
Effective length of database: 460
Effective search space:   207460
Effective search space used:   207460
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 Ga0059261_0082 Ga0059261_0082 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A (EC 6.3.5.-))
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.22209.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-170  554.1   0.0   1.4e-170  553.9   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0082  Ga0059261_0082 aspartyl/glutamyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0082  Ga0059261_0082 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A (
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.9   0.0  1.4e-170  1.4e-170       5     463 ..      16     483 ..      12     486 .. 0.96

  Alignments for each domain:
  == domain 1  score: 553.9 bits;  conditional E-value: 1.4e-170
                                 TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKdnia 70 
                                               + + e+++ ev+++++ +++a k+ +naf+  t+++a+++a+  d++ a  ++ k+lag+pi++Kd ++
  lcl|FitnessBrowser__Korea:Ga0059261_0082  16 VRSGEFTAIEVADAFITKVSAAKQ-LNAFIVETPDHAIAAARTADAARAagETlKPLAGVPIGMKDLFC 83 
                                               566778889999********9999.********************9888865567************** PP

                                 TIGR00132  71 vkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP......en 133
                                               +k+++tt+aS++Le+++++y++tV ++l +aga ++Gk NlD FamGss etS+fg +  P       n
  lcl|FitnessBrowser__Korea:Ga0059261_0082  84 TKGVQTTAASHMLEGFTPVYESTVSQKLWDAGAGMLGKLNLDQFAMGSSNETSYFGNVISPwrrkdgGN 152
                                               *************************************************************43333335 PP

                                 TIGR00132 134 eervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGi 202
                                                +  pGGSsgGs+ a+aa lvp a g+DTGgSiRqPA+f+g+ G+KPtYG+ SR+G+va+asSldq G+
  lcl|FitnessBrowser__Korea:Ga0059261_0082 153 AALAPGGSSGGSSSAIAARLVPAATGTDTGGSIRQPAAFTGISGIKPTYGRCSRWGVVAFASSLDQAGP 221
                                               6789***************************************************************** PP

                                 TIGR00132 203 lakkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekll 271
                                               +a++v d a++l++++g D kD tsl+++v+++   l +dl+g kvg+ ke++ ++++ e+++ +++ +
  lcl|FitnessBrowser__Korea:Ga0059261_0082 222 MARDVRDCAIMLEAMAGFDPKDATSLDMAVPNWEAGLSADLRGKKVGIPKEYRVDGMPAEIEALWQQGI 290
                                               ********************************************************************* PP

                                 TIGR00132 272 ekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrve.elkslkelyaktRsegfg 339
                                               + l++ gaeivevslp+ k+al++Yyii+p+Eassnlarydg+ryG+r   +  +l+e+ya+tR++gfg
  lcl|FitnessBrowser__Korea:Ga0059261_0082 291 DWLKDAGAEIVEVSLPHTKYALPAYYIIAPAEASSNLARYDGVRYGQRDLpDGANLQEMYAATRAAGFG 359
                                               ************************************************7526667************** PP

                                 TIGR00132 340 eevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplem 408
                                                ev+rRi++G+y+ls++ yd+yy++Aqkvrtli+++fek++ ++D++++ptap  af lgek +dpl+m
  lcl|FitnessBrowser__Korea:Ga0059261_0082 360 PEVQRRILIGTYVLSAGFYDAYYTQAQKVRTLIAQDFEKAWAQCDLLLTPTAPSAAFALGEKSADPLAM 428
                                               ********************************************************************* PP

                                 TIGR00132 409 ylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               yl+Dv+tvp +laG+pa+svP g +++glp+Glqiigk fd++ +l+++ a+eq+
  lcl|FitnessBrowser__Korea:Ga0059261_0082 429 YLNDVFTVPSSLAGIPAMSVPGGLDKDGLPLGLQIIGKPFDEQGVLNASLAIEQR 483
                                               ****************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (494 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.41
//
[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