Alignments for a candidate for gatB in Chlorobaculum tepidum TLS

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Chlorobaculum tepidum TLS

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate NP_663089.1 CT2215 aspartyl/glutamyl-tRNA amidotransferase subunit B

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000006985.1:NP_663089.1
          Length = 475

 Score =  462 bits (1188), Expect = e-134
 Identities = 226/474 (47%), Positives = 325/474 (68%), Gaps = 1/474 (0%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M++E V+GLEVH +L T+SK F    A FG   N+N   + LA PG LPV+N R V+ A+
Sbjct: 1   MNYEIVVGLEVHCQLNTESKAFCGCSAKFGKPANTNVCPVCLALPGALPVLNARVVEDAV 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITR 120
           +  +A N  IA  S   RKNYFYPD PK YQISQ+++PI   G I I+++   K + + R
Sbjct: 61  KLGLATNCTIARHSILARKNYFYPDLPKGYQISQYEEPICSEGVIHIDLEEGGKDVRLVR 120

Query: 121 LHMEEDAGKSTHK-GEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179
           +H+EEDAGKS H  G+ + +D+NR G PL+EIVS PD+R+PKEA AYL+KLR I++Y G+
Sbjct: 121 IHIEEDAGKSIHDIGDDTYIDVNRCGVPLLEIVSYPDMRTPKEASAYLQKLRQIVRYLGI 180

Query: 180 SDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGG 239
           SD  MEEGSLRCDAN+S+RP G  ++GT+ E+KN+NSF  V + +EYE KR  E +  GG
Sbjct: 181 SDGNMEEGSLRCDANVSVRPVGATEYGTRTEIKNMNSFRNVERAIEYEAKRHIEVIEGGG 240

Query: 240 EIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDER 299
            I QETR +D    +T  MR KE + DYRYFP+PD+VP+ +DD    R+++ +PE P++R
Sbjct: 241 TIVQETRLWDADKLETRSMRGKEHAHDYRYFPDPDLVPVLVDDGMIRRMQEELPEFPEDR 300

Query: 300 KAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVEL 359
            A++V+E G+PAYDA V+T+ +E++D+FEST++   D K +SNW+MG V   L +  +++
Sbjct: 301 AARFVSEFGIPAYDAGVITVDRELADYFESTVKVSGDAKASSNWVMGEVMRTLKEKYLDI 360

Query: 360 LDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLL 419
               ++PE L G+IKLI  G +S+ IAK+VF  +      A+ I+E  GL Q+SD   + 
Sbjct: 361 HKFAISPERLGGLIKLINAGAISNTIAKQVFEIMQQDEATAEAIVEREGLAQVSDRGAIE 420

Query: 420 KFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQELD 473
             + E L+ N++ +E Y++GK +  GF VGQ M+  KG+ANP++VN +L+  LD
Sbjct: 421 AAIREILEANQKQLEQYRSGKTQLFGFFVGQCMQKMKGKANPKMVNDILRSMLD 474


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: 630
Number of extensions: 28
Number of successful extensions: 2
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: 475
Length adjustment: 33
Effective length of query: 442
Effective length of database: 442
Effective search space:   195364
Effective search space used:   195364
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 NP_663089.1 CT2215 (aspartyl/glutamyl-tRNA amidotransferase subunit B)
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.26626.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   8.3e-184  597.5   0.0   9.3e-184  597.3   0.0    1.0  1  lcl|NCBI__GCF_000006985.1:NP_663089.1  CT2215 aspartyl/glutamyl-tRNA am


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000006985.1:NP_663089.1  CT2215 aspartyl/glutamyl-tRNA amidotransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  597.3   0.0  9.3e-184  9.3e-184       2     480 ..       1     473 [.       1     474 [. 0.99

  Alignments for each domain:
  == domain 1  score: 597.3 bits;  conditional E-value: 9.3e-184
                              TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskiv 73 
                                            ++ye+v+GlEvH+qlnt+sK Fc cs ++ + + Ntnvcpvcl+lPGalPvlN ++v+ A+kl+la+n+ i 
  lcl|NCBI__GCF_000006985.1:NP_663089.1   1 MNYEIVVGLEVHCQLNTESKAFCGCSAKFGK-PANTNVCPVCLALPGALPVLNARVVEDAVKLGLATNCTIA 71 
                                            69****************************9.99************************************65 PP

                              TIGR00133  74 sevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkdkqsl 145
                                               s+ +RK+YfYpDlPkgyqi+q++ Pi+++G+++i+lee+ k +++ r+h+EeD+gks +   d    ++
  lcl|NCBI__GCF_000006985.1:NP_663089.1  72 -RHSILARKNYFYPDLPKGYQISQYEEPICSEGVIHIDLEEGGKDVRLVRIHIEEDAGKSIHDIGD---DTY 139
                                            .69***********************************************************9776...69* PP

                              TIGR00133 146 vDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvE 217
                                            +D NR+gvPLlEiV+ Pd++++kea a+l+klrqi+ryl+isdg++eeGs+R+D+Nvs+r++G ++ gtr E
  lcl|NCBI__GCF_000006985.1:NP_663089.1 140 IDVNRCGVPLLEIVSYPDMRTPKEASAYLQKLRQIVRYLGISDGNMEEGSLRCDANVSVRPVGATEYGTRTE 211
                                            ************************************************************************ PP

                              TIGR00133 218 iKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieide 289
                                            iKN+ns++++e+aieyE +R +++++ g +++qetr +d  k  t s+R Ke+++DYRYfp+Pdl+p+ +d+
  lcl|NCBI__GCF_000006985.1:NP_663089.1 212 IKNMNSFRNVERAIEYEAKRHIEVIEGGGTIVQETRLWDADKLETRSMRGKEHAHDYRYFPDPDLVPVLVDD 283
                                            ************************************************************************ PP

                              TIGR00133 290 evvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLn 361
                                             ++++ ++e+lpe+Pe + +r+++e+g+ ++da v++ d+el+d+fe+ vk+++++k++ nW++ e++++L+
  lcl|NCBI__GCF_000006985.1:NP_663089.1 284 GMIRR-MQEELPEFPEDRAARFVSEFGIPAYDAGVITVDRELADYFESTVKVSGDAKASSNWVMGEVMRTLK 354
                                            ****9.****************************************************************** PP

                              TIGR00133 362 kkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveev 433
                                            +k +++++++++pe l  likli++g is+++ak+++e + +++  +++++e++gl q+sd+ ++ ++++e+
  lcl|NCBI__GCF_000006985.1:NP_663089.1 355 EKYLDIHKFAISPERLGGLIKLINAGAISNTIAKQVFEIMQQDEATAEAIVEREGLAQVSDRGAIEAAIREI 426
                                            ************************************************************************ PP

                              TIGR00133 434 ikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                            ++ n+k++e+y+sgk ++++f+vGq m+k kg+a+pk v+ +l+ +l
  lcl|NCBI__GCF_000006985.1:NP_663089.1 427 LEANQKQLEQYRSGKTQLFGFFVGQCMQKMKGKANPKMVNDILRSML 473
                                            ********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (475 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 0.02s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 5.09
//
[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