Alignments for a candidate for gatA in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Methylobacterium nodulans ORS 2060

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_015929904.1 MNOD_RS15675 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000022085.1:WP_015929904.1
          Length = 497

 Score =  433 bits (1113), Expect = e-126
 Identities = 235/445 (52%), Positives = 303/445 (68%), Gaps = 10/445 (2%)

Query: 39  KVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILEN 98
           K+ A+L    ERA A A+  D  +    E   L G+P+G+KD   T  + TT  SKILE 
Sbjct: 43  KLNAYLIETPERALAMAEVADRKI-AAGEARPLEGLPLGIKDLFCTHDVPTTAGSKILEG 101

Query: 99  FDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTENSAYKLTKNPW-----NLDTVPGG 153
           F P Y++TV   L    AV +GKLN+DEFAMGSS E SAY    +PW     +   VPGG
Sbjct: 102 FRPHYESTVSHNLWRDGAVMLGKLNLDEFAMGSSNETSAYGPVISPWRRRDSDAPLVPGG 161

Query: 154 SSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQI 213
           SSGGSAAAVAA     +  +DTGGSIRQPA+F G VG+KPTYGR SR+G+VAFASSLDQ 
Sbjct: 162 SSGGSAAAVAARLCLGATATDTGGSIRQPAAFTGTVGIKPTYGRCSRWGIVAFASSLDQA 221

Query: 214 GPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVG 273
           GPI RTV D A LL +++G D  D+T  +  VPD+  ++   +KGL I +PKEY  +G+ 
Sbjct: 222 GPIARTVRDTAILLTSMAGHDPKDTTCVDRPVPDYEKAVGRGVKGLTIGIPKEYRVDGMP 281

Query: 274 KEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSSSEASANLARFDGIRYGYRT 333
            E         + L+  GAT  EVSLPH++YAL  YY+++ +EAS+NLAR+DG+RYG R 
Sbjct: 282 AEIERLWHQGAEWLKAAGATIVEVSLPHTQYALPAYYIVAPAEASSNLARYDGVRYGLRV 341

Query: 334 DNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVF 393
             A +++ +Y+QTRA GFG EVKRRIM+GT+ LS+GYYDAYY +AQK+RTLIK+DFE V+
Sbjct: 342 P-AKDIVGMYEQTRAAGFGREVKRRIMIGTYVLSAGYYDAYYVRAQKIRTLIKRDFEAVY 400

Query: 394 EK-YDVIVGPTTPTPAFKIGE-NTKDPLTMYANDILTIPVNLAGVPGISVPCGL-ADGLP 450
               D I+ P TP+ AF IGE    DP+ MY ND+ T+ VN+AG+PGI+VP GL A GLP
Sbjct: 401 ANGVDAILTPATPSAAFGIGEKQNADPVEMYLNDVFTVTVNMAGLPGIAVPAGLDAQGLP 460

Query: 451 LGLQIIGKHFDESTVYRVAHAFEQA 475
           LGLQ+IG+ FDE T++      E+A
Sbjct: 461 LGLQLIGRPFDEETLFAAGQVIEEA 485


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: 617
Number of extensions: 38
Number of successful extensions: 6
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: 497
Length adjustment: 34
Effective length of query: 451
Effective length of database: 463
Effective search space:   208813
Effective search space used:   208813
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_015929904.1 MNOD_RS15675 (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.23287.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-169  550.2   0.0   2.2e-169  550.0   0.0    1.0  1  lcl|NCBI__GCF_000022085.1:WP_015929904.1  MNOD_RS15675 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000022085.1:WP_015929904.1  MNOD_RS15675 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 !  550.0   0.0  2.2e-169  2.2e-169       5     463 ..      20     485 ..      16     488 .. 0.97

  Alignments for each domain:
  == domain 1  score: 550.0 bits;  conditional E-value: 2.2e-169
                                 TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniav 71 
                                               l +k++s++e++++ l+++ + ++ +na+l  t+e+al++a+  d+k+a  e ++l g+p+++Kd +++
  lcl|NCBI__GCF_000022085.1:WP_015929904.1  20 LRQKSFSAREITQAHLDAVAQARK-LNAYLIETPERALAMAEVADRKIAaGEaRPLEGLPLGIKDLFCT 87 
                                               6789999************99998.***********************986647*************** PP

                                 TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....enee 135
                                               +d++tt++SkiLe++++ y++tV ++l ++ga+++Gk NlDEFamGss etSa+g++  P      +  
  lcl|NCBI__GCF_000022085.1:WP_015929904.1  88 HDVPTTAGSKILEGFRPHYESTVSHNLWRDGAVMLGKLNLDEFAMGSSNETSAYGPVISPwrrrdSDAP 156
                                               ************************************************************444333556 PP

                                 TIGR00132 136 rvpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGila 204
                                                vpGGSsgGsaaavaa l+  a ++DTGgSiRqPA+f+g+vG+KPtYG+ SR+G+va+asSldq G++a
  lcl|NCBI__GCF_000022085.1:WP_015929904.1 157 LVPGGSSGGSAAAVAARLCLGATATDTGGSIRQPAAFTGTVGIKPTYGRCSRWGIVAFASSLDQAGPIA 225
                                               8******************************************************************** PP

                                 TIGR00132 205 kkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllek 273
                                               ++v d+a++l  ++g+D kD+t ++ +v+++ +++ + +kgl +g+ ke++ ++++ e+++ +++  e 
  lcl|NCBI__GCF_000022085.1:WP_015929904.1 226 RTVRDTAILLTSMAGHDPKDTTCVDRPVPDYEKAVGRGVKGLTIGIPKEYRVDGMPAEIERLWHQGAEW 294
                                               ********************************************************************* PP

                                 TIGR00132 274 leelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeev 342
                                               l++ ga+ivevslp+ ++al++Yyi++p+Eassnlarydg+ryG rv  ++ +  +y +tR++gfg+ev
  lcl|NCBI__GCF_000022085.1:WP_015929904.1 295 LKAAGATIVEVSLPHTQYALPAYYIVAPAEASSNLARYDGVRYGLRVPAKD-IVGMYEQTRAAGFGREV 362
                                               ***********************************************9998.***************** PP

                                 TIGR00132 343 krRimlGayalskeyydkyykkAqkvrtliidefeklf.eevDvivsptaptlafklgekaed.plemy 409
                                               krRim+G+y+ls++yyd+yy +Aqk+rtli+++fe ++ + vD i++p++p  af +gek++  p+emy
  lcl|NCBI__GCF_000022085.1:WP_015929904.1 363 KRRIMIGTYVLSAGYYDAYYVRAQKIRTLIKRDFEAVYaNGVDAILTPATPSAAFGIGEKQNAdPVEMY 431
                                               *************************************9557******************98755***** PP

                                 TIGR00132 410 lsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               l+Dv+tv++n+aGlp+i+vP+g + +glp+Glq+ig+ fd+++l+ +++ +e+a
  lcl|NCBI__GCF_000022085.1:WP_015929904.1 432 LNDVFTVTVNMAGLPGIAVPAGLDAQGLPLGLQLIGRPFDEETLFAAGQVIEEA 485
                                               ************************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (497 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: 9.20
//
[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