Alignments for a candidate for gatA in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Cupriavidus basilensis 4G11

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate RR42_RS00590 RR42_RS00590 glutamyl-tRNA amidotransferase

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__Cup4G11:RR42_RS00590
          Length = 501

 Score =  467 bits (1202), Expect = e-136
 Identities = 246/490 (50%), Positives = 333/490 (67%), Gaps = 16/490 (3%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           + EL   +  + +   +L  +   RI+     + AF+ ++ E   A A+  D A   R E
Sbjct: 11  LRELSDALAARSVSAEELARDYLARIEQAG-ALNAFVDVNPELTLAQARAAD-ARRARGE 68

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            G L G+PI  KD  VT+G R T  S++L N++  +DA VV+RL  A  VT+GK NMDEF
Sbjct: 69  AGPLTGVPIAHKDVFVTRGWRATAGSRMLANYESPFDAAVVERLAAAGMVTLGKTNMDEF 128

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSS ENS +   +NPW+   VPGGSSGGSAAAVAAG  P + G+DTGGSIRQPASF G
Sbjct: 129 AMGSSNENSHFGPVRNPWDASRVPGGSSGGSAAAVAAGLAPAATGTDTGGSIRQPASFSG 188

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTS---ANVD 244
           + G+KPTYGRVSRYG++AFASSLDQ GP+  T ED A LL  ++G D+ DSTS   A   
Sbjct: 189 ITGIKPTYGRVSRYGMIAFASSLDQGGPMAHTAEDCAMLLGGMAGFDERDSTSVAPALGG 248

Query: 245 VPDFLSSLTGD----------IKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATW 294
           V +  + L G           + GL+I +PKEY G+G+  +  ++V AAL   E LGAT 
Sbjct: 249 VDEDYTRLLGQARAGASAGKPLSGLRIGLPKEYFGKGLAADVEQAVRAALAEYEKLGATL 308

Query: 295 EEVSLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNE 354
            EVSLP ++ ++  YY+++ +EAS+NL+RFDG+R+G+R     +L+D+YK+TRAEGFG E
Sbjct: 309 VEVSLPKTELSIPVYYVIAPAEASSNLSRFDGVRFGHRAAEYRDLMDMYKKTRAEGFGPE 368

Query: 355 VKRRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGEN 414
           VKRRIM+G + LS GYYDAYY +AQK+R +I  DF+  F + DVI+GP  PT A+K+GE 
Sbjct: 369 VKRRIMVGAYVLSHGYYDAYYLQAQKIRRIIADDFQRAFTQCDVIMGPVAPTVAWKLGEK 428

Query: 415 TKDPLTMYANDILTIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFE 473
           + DP+ MY  DI T+  +LAG+PG+SVPCGL + G+P+GLQ+IG +F E+ + + AHAF+
Sbjct: 429 SADPVQMYLADIFTLSTSLAGLPGMSVPCGLGEGGMPVGLQLIGNYFGEAELLQTAHAFQ 488

Query: 474 QATDHHKAKP 483
           QATD H  +P
Sbjct: 489 QATDWHLRRP 498


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: 595
Number of extensions: 21
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: 501
Length adjustment: 34
Effective length of query: 451
Effective length of database: 467
Effective search space:   210617
Effective search space used:   210617
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 RR42_RS00590 RR42_RS00590 (glutamyl-tRNA amidotransferase)
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.19522.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.9e-179  582.2   0.0   5.1e-179  581.8   0.0    1.1  1  lcl|FitnessBrowser__Cup4G11:RR42_RS00590  RR42_RS00590 glutamyl-tRNA amido


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS00590  RR42_RS00590 glutamyl-tRNA amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.8   0.0  5.1e-179  5.1e-179       3     465 ..      16     492 ..      14     493 .. 0.95

  Alignments for each domain:
  == domain 1  score: 581.8 bits;  conditional E-value: 5.1e-179
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdni 69 
                                               ++l +++vs++e+++++l+rie+    +naf++v++e +l++a++ d++ a  e  +l+g+pia Kd++
  lcl|FitnessBrowser__Cup4G11:RR42_RS00590  16 DALAARSVSAEELARDYLARIEQAGA-LNAFVDVNPELTLAQARAADARRArGEaGPLTGVPIAHKDVF 83 
                                               6788999****************999.*********************99975646************* PP

                                 TIGR00132  70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervp 138
                                               ++++++ t++S++L ny sp+da Vverl +ag++++GktN+DEFamGss e+S fg+++nP++ +rvp
  lcl|FitnessBrowser__Cup4G11:RR42_RS00590  84 VTRGWRATAGSRMLANYESPFDAAVVERLAAAGMVTLGKTNMDEFAMGSSNENSHFGPVRNPWDASRVP 152
                                               ********************************************************************* PP

                                 TIGR00132 139 GGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkv 207
                                               GGSsgGsaaavaa+l+p a g+DTGgSiRqPAsf+g+ G+KPtYG+vSRyG++a+asSldq G++a++ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS00590 153 GGSSGGSAAAVAAGLAPAATGTDTGGSIRQPASFSGITGIKPTYGRVSRYGMIAFASSLDQGGPMAHTA 221
                                               ********************************************************************* PP

                                 TIGR00132 208 edialvldvisgkDkkDstslevk....veelleelkk.........dlkglkvgvvkelseesldkev 263
                                               ed a++l  ++g D++Dsts+  +    +e++++ l +          l gl++g+ ke+++++l  +v
  lcl|FitnessBrowser__Cup4G11:RR42_RS00590 222 EDCAMLLGGMAGFDERDSTSVAPAlggvDEDYTRLLGQaragasagkPLSGLRIGLPKEYFGKGLAADV 290
                                               ********************9754122133444332222235554546789****************** PP

                                 TIGR00132 264 kekfekllekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyak 332
                                               +++++++l + e+lga++vevslp+ +l++++Yy+i+p+Eassnl+r+dg+r+G+r+ e+++l+++y+k
  lcl|FitnessBrowser__Cup4G11:RR42_RS00590 291 EQAVRAALAEYEKLGATLVEVSLPKTELSIPVYYVIAPAEASSNLSRFDGVRFGHRAAEYRDLMDMYKK 359
                                               ********************************************************************* PP

                                 TIGR00132 333 tRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgek 401
                                               tR+egfg evkrRim+Gay+ls++yyd+yy++Aqk+r++i+d+f+ +f+++Dvi++p+apt+a klgek
  lcl|FitnessBrowser__Cup4G11:RR42_RS00590 360 TRAEGFGPEVKRRIMVGAYVLSHGYYDAYYLQAQKIRRIIADDFQRAFTQCDVIMGPVAPTVAWKLGEK 428
                                               ********************************************************************* PP

                                 TIGR00132 402 aedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                                +dp++myl+D++t+  +laGlp++svP+g  e g+p+Glq+ig++f + +ll+ a+a++qa+d
  lcl|FitnessBrowser__Cup4G11:RR42_RS00590 429 SADPVQMYLADIFTLSTSLAGLPGMSVPCGLGEGGMPVGLQLIGNYFGEAELLQTAHAFQQATD 492
                                               ************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (501 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: 9.03
//
[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