Alignments for a candidate for gatA in Thiomicrorhabdus chilensis DSM 12352

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Thiomicrorhabdus chilensis DSM 12352

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_028486148.1 B076_RS0103865 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000483485.1:WP_028486148.1
          Length = 484

 Score =  493 bits (1268), Expect = e-144
 Identities = 244/476 (51%), Positives = 330/476 (69%), Gaps = 1/476 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I ++ + +H  EI    L      RI   D ++ A++++  E A   A++ D+ +    E
Sbjct: 6   IKQMSEKLHAGEITSVQLTQHYLDRISKYDTELNAYVSVTPELAMMMAEQADKKL-ASGE 64

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
             LL G+P+  KD   T G++T+CSSK+L+NF   YDA VV +L+      +GK NMDEF
Sbjct: 65  ADLLTGIPVAHKDIFCTDGVKTSCSSKMLDNFIAPYDAHVVSQLKKVGMPILGKTNMDEF 124

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSS+E+S Y  TKNPWN   VPGGSSGG+AA +AAG  P + G+DTGGSIRQPASFCG
Sbjct: 125 AMGSSSESSYYGPTKNPWNHQAVPGGSSGGAAAVIAAGLAPMATGTDTGGSIRQPASFCG 184

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           + G+KPTYG VSR+G+VA+ASS DQ GP+TR+ +D+A+LL A++G D+ DSTS   +  D
Sbjct: 185 ITGIKPTYGSVSRFGIVAYASSFDQAGPMTRSAQDSAWLLNAMAGFDERDSTSLQREAVD 244

Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALA 307
           + + L   +KGLK+ VP EY GEG+  +    V  A+  +E LGA   EV LP+   A+ 
Sbjct: 245 YAAELGQSLKGLKVGVPAEYFGEGLDADVEAVVRDAIAEVEKLGAEVVEVHLPNKDLAVP 304

Query: 308 TYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALS 367
           +YY+L+ +EAS+NL+RFDG+R+GYR +N  +L DLYK++R+EG G EVKRRIM+G +ALS
Sbjct: 305 SYYVLAPAEASSNLSRFDGVRFGYRCENPKDLEDLYKRSRSEGLGAEVKRRIMVGAYALS 364

Query: 368 SGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDIL 427
           +GYYDAYY KAQK+R +++ DF   FE  DVI+GP  PTPAF IGE T DP +MY  D+ 
Sbjct: 365 AGYYDAYYLKAQKLRRMVRDDFTKAFESCDVIMGPVAPTPAFNIGEKTDDPTSMYLADLY 424

Query: 428 TIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483
           TIPVNLAG+PGISVP G  +  P+GL I+G +F E+ +  VAH ++Q TD H   P
Sbjct: 425 TIPVNLAGLPGISVPAGFVNDRPVGLHIVGPYFSETKLLNVAHQYQQVTDWHTRMP 480


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: 605
Number of extensions: 24
Number of successful extensions: 1
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: 484
Length adjustment: 34
Effective length of query: 451
Effective length of database: 450
Effective search space:   202950
Effective search space used:   202950
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 WP_028486148.1 B076_RS0103865 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
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.7496.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.7e-191  620.8   0.0     9e-191  620.5   0.0    1.0  1  lcl|NCBI__GCF_000483485.1:WP_028486148.1  B076_RS0103865 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000483485.1:WP_028486148.1  B076_RS0103865 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  620.5   0.0    9e-191    9e-191       3     465 ..      11     474 ..       9     475 .. 0.99

  Alignments for each domain:
  == domain 1  score: 620.5 bits;  conditional E-value: 9e-191
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdni 69 
                                               e+l++ e++++++++++l+ri++ + ++na+++vt+e a+ +a++ dkk+a  e ++l+gip+a Kd +
  lcl|NCBI__GCF_000483485.1:WP_028486148.1  11 EKLHAGEITSVQLTQHYLDRISKYDTELNAYVSVTPELAMMMAEQADKKLAsGEaDLLTGIPVAHKDIF 79 
                                               6789999*******************************************985647************* PP

                                 TIGR00132  70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervp 138
                                               ++ +++t+c+Sk+L+n+++pyda+Vv +lk+ g+ i+GktN+DEFamGss+e+S++g+tknP+n++ vp
  lcl|NCBI__GCF_000483485.1:WP_028486148.1  80 CTDGVKTSCSSKMLDNFIAPYDAHVVSQLKKVGMPILGKTNMDEFAMGSSSESSYYGPTKNPWNHQAVP 148
                                               ********************************************************************* PP

                                 TIGR00132 139 GGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkv 207
                                               GGSsgG+aa++aa+l+p+a g+DTGgSiRqPAsfcg+ G+KPtYG vSR+G+vayasS+dq G+++++ 
  lcl|NCBI__GCF_000483485.1:WP_028486148.1 149 GGSSGGAAAVIAAGLAPMATGTDTGGSIRQPASFCGITGIKPTYGSVSRFGIVAYASSFDQAGPMTRSA 217
                                               ********************************************************************* PP

                                 TIGR00132 208 edialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfeklleklee 276
                                               +d a +l++++g D++Dstsl+ +  ++  el + lkglkvgv  e+++e+ld +v++ +++++ ++e+
  lcl|NCBI__GCF_000483485.1:WP_028486148.1 218 QDSAWLLNAMAGFDERDSTSLQREAVDYAAELGQSLKGLKVGVPAEYFGEGLDADVEAVVRDAIAEVEK 286
                                               ********************************************************************* PP

                                 TIGR00132 277 lgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrR 345
                                               lgae+vev+lp+ +la++ Yy+++p+Eassnl+r+dg+r+G+r e++k+l++ly+++Rseg+g+evkrR
  lcl|NCBI__GCF_000483485.1:WP_028486148.1 287 LGAEVVEVHLPNKDLAVPSYYVLAPAEASSNLSRFDGVRFGYRCENPKDLEDLYKRSRSEGLGAEVKRR 355
                                               ********************************************************************* PP

                                 TIGR00132 346 imlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvl 414
                                               im+Gayals++yyd+yy+kAqk+r++++d+f+k+fe++Dvi++p+apt af++gek++dp +myl+D++
  lcl|NCBI__GCF_000483485.1:WP_028486148.1 356 IMVGAYALSAGYYDAYYLKAQKLRRMVRDDFTKAFESCDVIMGPVAPTPAFNIGEKTDDPTSMYLADLY 424
                                               ********************************************************************* PP

                                 TIGR00132 415 tvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               t+p+nlaGlp+isvP+g   ++ p+Gl i+g +f+++kll+va++++q +d
  lcl|NCBI__GCF_000483485.1:WP_028486148.1 425 TIPVNLAGLPGISVPAGFV-NDRPVGLHIVGPYFSETKLLNVAHQYQQVTD 474
                                               *******************.7*************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (484 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: 11.50
//
[ok]

This GapMind analysis is from Apr 10 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