Alignments for a candidate for gatA in Methylobacterium sp. 4-46

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Methylobacterium sp. 4-46

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_012334070.1 M446_RS20750 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000019365.1:WP_012334070.1
          Length = 497

 Score =  429 bits (1103), Expect = e-124
 Identities = 230/444 (51%), Positives = 301/444 (67%), Gaps = 10/444 (2%)

Query: 40  VQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENF 99
           + A+L    ERA A A+  D  +    E   L G+P+G+KD   T  + TT  S+ILE F
Sbjct: 44  LNAYLIETPERALAMAEVADRKI-AAGEARPLEGLPLGIKDLFCTHDVPTTAGSRILEGF 102

Query: 100 DPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTENSAYKLTKNPWN-----LDTVPGGS 154
            P Y++TV   L    AV +GKLN+DEFAMGSS E SAY    +PW         VPGGS
Sbjct: 103 RPHYESTVSHNLWRDGAVMLGKLNLDEFAMGSSNETSAYGPVVSPWRRRDSEAPLVPGGS 162

Query: 155 SGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIG 214
           SGGSAAAVAA     +  +DTGGSIRQPA+F G VG+KPTYGR SR+G+VAFASSLDQ G
Sbjct: 163 SGGSAAAVAARLCLGATATDTGGSIRQPAAFTGTVGIKPTYGRCSRWGIVAFASSLDQAG 222

Query: 215 PITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGK 274
           PITRTV D+A +L +++G D  D+T  +  VPD+ ++++  +KGL I +PKEY  +G+  
Sbjct: 223 PITRTVRDSAIMLASMAGHDPKDTTCVDRPVPDYEAAVSRGVKGLTIGIPKEYRVDGMPA 282

Query: 275 EARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTD 334
           E         + L   GA   EVSLPH++YAL  YY+++ +EAS+NLAR+DG+RYG R  
Sbjct: 283 EIERLWHQGAEWLRAAGARIVEVSLPHTRYALPAYYIVAPAEASSNLARYDGVRYGLRVP 342

Query: 335 NADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFE 394
             D ++ +Y+QTRA GFG EVKRRIM+GT+ LS+GYYDAYY +AQK+RTLIK+DFE V+ 
Sbjct: 343 GKD-IVGMYEQTRAAGFGREVKRRIMIGTYVLSAGYYDAYYVRAQKIRTLIKRDFETVYA 401

Query: 395 K-YDVIVGPTTPTPAFKIGE-NTKDPLTMYANDILTIPVNLAGVPGISVPCGL-ADGLPL 451
              D I+ P TP+ AF +GE    DP+ MY ND+ T+ VN+AG+PGI+VP GL   GLPL
Sbjct: 402 NGVDAILTPATPSAAFGLGEKQNADPVEMYLNDVFTVTVNMAGLPGIAVPAGLDGQGLPL 461

Query: 452 GLQIIGKHFDESTVYRVAHAFEQA 475
           GLQ+IG+ FDE T++      E+A
Sbjct: 462 GLQLIGRPFDEETLFAAGQVIEEA 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: 614
Number of extensions: 36
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_012334070.1 M446_RS20750 (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.24100.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-166  540.7   0.0   1.7e-166  540.5   0.0    1.0  1  lcl|NCBI__GCF_000019365.1:WP_012334070.1  M446_RS20750 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019365.1:WP_012334070.1  M446_RS20750 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 !  540.5   0.0  1.7e-166  1.7e-166       5     463 ..      20     485 ..      16     488 .. 0.96

  Alignments for each domain:
  == domain 1  score: 540.5 bits;  conditional E-value: 1.7e-166
                                 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_000019365.1:WP_012334070.1  20 LRRKAFSAREIAQAHLDAVARARA-LNAYLIETPERALAMAEVADRKIAaGEaRPLEGLPLGIKDLFCT 87 
                                               678899999**********99998.***********************986647*************** PP

                                 TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....enee 135
                                               +d++tt++S+iLe++++ y++tV ++l ++ga+++Gk NlDEFamGss etSa+g++  P      +  
  lcl|NCBI__GCF_000019365.1:WP_012334070.1  88 HDVPTTAGSRILEGFRPHYESTVSHNLWRDGAVMLGKLNLDEFAMGSSNETSAYGPVVSPwrrrdSEAP 156
                                               ************************************************************444333445 PP

                                 TIGR00132 136 rvpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGila 204
                                                vpGGSsgGsaaavaa l+  a ++DTGgSiRqPA+f+g+vG+KPtYG+ SR+G+va+asSldq G+++
  lcl|NCBI__GCF_000019365.1:WP_012334070.1 157 LVPGGSSGGSAAAVAARLCLGATATDTGGSIRQPAAFTGTVGIKPTYGRCSRWGIVAFASSLDQAGPIT 225
                                               8******************************************************************** PP

                                 TIGR00132 205 kkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllek 273
                                               ++v d a++l+ ++g+D kD+t ++ +v+++  ++ + +kgl +g+ ke++ ++++ e+++ +++  e 
  lcl|NCBI__GCF_000019365.1:WP_012334070.1 226 RTVRDSAIMLASMAGHDPKDTTCVDRPVPDYEAAVSRGVKGLTIGIPKEYRVDGMPAEIERLWHQGAEW 294
                                               ********************************************************************* PP

                                 TIGR00132 274 leelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeev 342
                                               l++ ga ivevslp+ ++al++Yyi++p+Eassnlarydg+ryG rv  ++ +  +y +tR++gfg+ev
  lcl|NCBI__GCF_000019365.1:WP_012334070.1 295 LRAAGARIVEVSLPHTRYALPAYYIVAPAEASSNLARYDGVRYGLRVPGKD-IVGMYEQTRAAGFGREV 362
                                               ***********************************************9998.***************** PP

                                 TIGR00132 343 krRimlGayalskeyydkyykkAqkvrtliidefeklf.eevDvivsptaptlafklgekaed.plemy 409
                                               krRim+G+y+ls++yyd+yy +Aqk+rtli+++fe ++ + vD i++p++p  af lgek++  p+emy
  lcl|NCBI__GCF_000019365.1:WP_012334070.1 363 KRRIMIGTYVLSAGYYDAYYVRAQKIRTLIKRDFETVYaNGVDAILTPATPSAAFGLGEKQNAdPVEMY 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_000019365.1:WP_012334070.1 432 LNDVFTVTVNMAGLPGIAVPAGLDGQGLPLGLQLIGRPFDEETLFAAGQVIEEA 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: 8.89
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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