Alignments for a candidate for gatB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate Echvi_3042 Echvi_3042 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__Cola:Echvi_3042
          Length = 487

 Score =  417 bits (1073), Expect = e-121
 Identities = 217/477 (45%), Positives = 312/477 (65%), Gaps = 6/477 (1%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E V+GLEVHV+L T SKM++     FG  PN+N +VI L +PG LP VNKRAV++AM+ 
Sbjct: 10  YELVVGLEVHVQLLTKSKMYASDSTEFGNLPNTNISVITLGHPGTLPKVNKRAVEFAMKL 69

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDI--EVDGETKRIGITR 120
            +A   EI   + F RKNYFYPD PK YQ++Q   P+   G + I  E  G T+ I +TR
Sbjct: 70  GLACKSEITRHNIFARKNYFYPDLPKGYQLTQDKNPVCVGGTVPITLEKSGVTREIELTR 129

Query: 121 LHMEEDAGKSTH-KGEY-SLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTG 178
           +HMEEDAGKS H  GE  +LVD NR G PL+EIV+EP IR+ +EAY ++ ++R +++Y  
Sbjct: 130 IHMEEDAGKSMHLAGEVDTLVDFNRAGVPLLEIVTEPCIRASEEAYQFMSEIRKLVRYLE 189

Query: 179 VSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSG 238
           + D  MEEGS+RCDANIS+R  G  + G K E+KN+NSF  V + +E+E  RQ + +  G
Sbjct: 190 ICDGNMEEGSMRCDANISIRLKGDTELGKKVEVKNMNSFRNVARAIEHEFDRQIDMMEKG 249

Query: 239 GEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDE 298
             I  ETR FD +TG T  MR KE  +DYRYFPEPD+ P+ I D W +++ +++P LP E
Sbjct: 250 ETIISETRTFDATTGLTAGMRTKEDLNDYRYFPEPDLSPVVISDEWLQQISESMPSLPRE 309

Query: 299 RKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVE 358
              ++VN  GLP YDA+VLT +KE++ +FE+      + K  SNW+MG V  YLN+  + 
Sbjct: 310 LHERFVNAFGLPEYDANVLTDSKEIALYFEALCGETNNYKAASNWMMGPVKSYLNELTLH 369

Query: 359 LLDTKLTPENLAGMIKLIEDGTMSSKIA-KKVFPELAAKGGNAK-QIMEDNGLVQISDEA 416
           + D  + P+ LA +I LI++G ++  +A +KV+PE+      +  +I +   L+Q SDE 
Sbjct: 370 IEDFPVRPKQLASLIALIDEGKVNFSVASQKVYPEMIKDPSQSPLEIAQKLNLIQESDEG 429

Query: 417 TLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQELD 473
           +L   V   L  NE  V +YK+GK   +G  +GQ+MK SKG+A+P++ N++L + L+
Sbjct: 430 SLKPIVESVLAENEAKVAEYKSGKKGLLGMFMGQVMKKSKGKADPKVANKILTELLE 486


Lambda     K      H
   0.313    0.133    0.373 

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: 652
Number of extensions: 27
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: 475
Length of database: 487
Length adjustment: 34
Effective length of query: 441
Effective length of database: 453
Effective search space:   199773
Effective search space used:   199773
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate Echvi_3042 Echvi_3042 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.22364.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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  553.9   0.1   1.5e-170  553.7   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_3042  Echvi_3042 aspartyl/glutamyl-tRN


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_3042  Echvi_3042 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.7   0.1  1.5e-170  1.5e-170       3     480 ..       9     485 ..       7     486 .. 0.97

  Alignments for each domain:
  == domain 1  score: 553.7 bits;  conditional E-value: 1.5e-170
                            TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsev 76 
                                          +yelv+GlEvHvql tksK++++ s+e+ +  pNtn++ + lg PG+lP +Nk+av++A+kl+la +s+i+   
  lcl|FitnessBrowser__Cola:Echvi_3042   9 KYELVVGLEVHVQLLTKSKMYASDSTEFGN-LPNTNISVITLGHPGTLPKVNKRAVEFAMKLGLACKSEIT-RH 80 
                                          79****************************.9*************************************66.69 PP

                            TIGR00133  77 svFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke..keigierlhlEeDtgksqykesdkdkqslvDf 148
                                           +F+RK+YfYpDlPkgyq+tq + P++ +G++ i le++   +ei+++r+h+EeD+gks++     ++ +lvDf
  lcl|FitnessBrowser__Cola:Echvi_3042  81 NIFARKNYFYPDLPKGYQLTQDKNPVCVGGTVPITLEKSGvtREIELTRIHMEEDAGKSMHLAG--EVDTLVDF 152
                                          9******************************98776665455********************66..589***** PP

                            TIGR00133 149 NRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNln 222
                                          NR+gvPLlEiVt+P ++ ++ea +f++++r+++rylei dg++eeGsmR+D+N+sirlkG+++ g++vE+KN+n
  lcl|FitnessBrowser__Cola:Echvi_3042 153 NRAGVPLLEIVTEPCIRASEEAYQFMSEIRKLVRYLEICDGNMEEGSMRCDANISIRLKGDTELGKKVEVKNMN 226
                                          ************************************************************************** PP

                            TIGR00133 223 slksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkekv 296
                                          s++++++aie+E  Rq+++++kge++  etr+fd ++  t  +R Ke+ +DYRYfpePdl p++i++e++++ +
  lcl|FitnessBrowser__Cola:Echvi_3042 227 SFRNVARAIEHEFDRQIDMMEKGETIISETRTFDATTGLTAGMRTKEDLNDYRYFPEPDLSPVVISDEWLQQ-I 299
                                          *********************************************************************999.* PP

                            TIGR00133 297 eeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaea 370
                                          +e +p lP++ ++r+++ +gl e+da+vl++ +e++ +fe +   +++ k+a nW++  ++++Ln+ ++ ++++
  lcl|FitnessBrowser__Cola:Echvi_3042 300 SESMPSLPRELHERFVNAFGLPEYDANVLTDSKEIALYFEALCGETNNYKAASNWMMGPVKSYLNELTLHIEDF 373
                                          ************************************************************************** PP

                            TIGR00133 371 llkpeelaeliklikegkisqksa.kelleellen.kkdpkklieklgliqisdekelvkiveevikenpkeve 442
                                           ++p++la+li+li+egk++   a +++  e++++  ++p ++++kl+liq sde  l+ ive v++en+ +v 
  lcl|FitnessBrowser__Cola:Echvi_3042 374 PVRPKQLASLIALIDEGKVNFSVAsQKVYPEMIKDpSQSPLEIAQKLNLIQESDEGSLKPIVESVLAENEAKVA 447
                                          ********************8876267999999988999*********************************** PP

                            TIGR00133 443 kyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                          +yksgk+ +l++++Gqvmkk+kg+adpk ++k+l ell
  lcl|FitnessBrowser__Cola:Echvi_3042 448 EYKSGKKGLLGMFMGQVMKKSKGKADPKVANKILTELL 485
                                          ************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (487 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: 00:00:00.03
# Mc/sec: 7.13
//
[ok]

This GapMind analysis is from Apr 09 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