Alignments for a candidate for gatA in Sphingomonas koreensis DSMZ 15582

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.19413.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.96
//
[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