Alignments for a candidate for gatB in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Sphingomonas koreensis DSMZ 15582

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate Ga0059261_0083 Ga0059261_0083 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (EC 6.3.5.-)

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__Korea:Ga0059261_0083
          Length = 486

 Score =  421 bits (1082), Expect = e-122
 Identities = 220/473 (46%), Positives = 313/473 (66%), Gaps = 4/473 (0%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E VIGLEVH ++ +++K+FS +   FGAEPN+  ++ID A PG+LPV N+  +  A+R 
Sbjct: 15  WEVVIGLEVHAQVTSNAKLFSGAATEFGAEPNTQVSLIDAAMPGMLPVPNRECIRQAVRT 74

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITRLH 122
            MA++ +I   S+FDRKNYFY D P+ YQISQ   P+   G I+IEVDGETK IG+ R+H
Sbjct: 75  GMAIDAQINKWSRFDRKNYFYADLPQGYQISQLYHPLVGEGEIEIEVDGETKTIGVERIH 134

Query: 123 MEEDAGKSTH--KGEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGVS 180
           +E+DAGK  H      S VDLNR G  L+EIVS+PD+RSP EA AYL KLRSI++Y G  
Sbjct: 135 VEQDAGKLMHDQHPRLSYVDLNRSGVALMEIVSKPDMRSPAEAGAYLSKLRSILRYVGSC 194

Query: 181 DVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGGE 240
           D  M++GS+R D N+S+R  G E FGT+ E KN+NS  +V + +E E  RQ + + SGG+
Sbjct: 195 DGNMDQGSMRADVNVSVRRPG-EAFGTRTETKNVNSVRFVMQTVEIEALRQIDVIESGGK 253

Query: 241 IGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDERK 300
           I QETR FD   G+T  MR KE + DYRYFP+PD++PL +DDA+ E  R ++PELPD ++
Sbjct: 254 IVQETRLFDPDKGETRSMRSKEDAHDYRYFPDPDLLPLELDDAFLEECRGSLPELPDAKR 313

Query: 301 AKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVELL 360
           A+Y+  LG+  Y+A VLT   E + +F++ ++ GA     +NW+   +   LNK   ++ 
Sbjct: 314 ARYL-ALGITPYNAGVLTAEVESARYFDALLDAGAKGPAAANWVTSELFGALNKLGKDIE 372

Query: 361 DTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLLK 420
           ++ ++P   A ++ L+ DGT+S  +AK+VF  +   GG+   I+E+ GL Q SD   +  
Sbjct: 373 NSPVSPAQAAELLGLVADGTISGSLAKQVFEIMLETGGSPSAIVEERGLKQTSDTGAIEA 432

Query: 421 FVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQELD 473
            + E L  N   +E Y+ GK    GF VGQ MKA  G+ANP +VN+LLK+ L+
Sbjct: 433 VIAEVLAKNPGQLEQYRGGKEALFGFFVGQTMKAMGGKANPGVVNELLKKALN 485


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: 635
Number of extensions: 22
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: 486
Length adjustment: 34
Effective length of query: 441
Effective length of database: 452
Effective search space:   199332
Effective search space used:   199332
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 Ga0059261_0083 Ga0059261_0083 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (EC 6.3.5.-))
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.31082.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.4e-163  528.2   0.0   9.6e-163  528.0   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0083  Ga0059261_0083 aspartyl/glutamyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0083  Ga0059261_0083 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.0   0.0  9.6e-163  9.6e-163       3     481 .]      14     485 ..      12     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 528.0 bits;  conditional E-value: 9.6e-163
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               e+e+viGlEvH q+  ++KlF+ + +e+   +pNt+v+ ++ ++PG lPv+N+e +++A+  ++a++++
  lcl|FitnessBrowser__Korea:Ga0059261_0083  14 EWEVVIGLEVHAQVTSNAKLFSGAATEFGA-EPNTQVSLIDAAMPGMLPVPNRECIRQAVRTGMAIDAQ 81 
                                               689*************************99.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140
                                               i+ + s FdRK+YfY DlP+gyqi+q + P++ +G++eie++++ k+ig+er+h+E+D+gk+++ ++  
  lcl|FitnessBrowser__Korea:Ga0059261_0083  82 IN-KWSRFDRKNYFYADLPQGYQISQLYHPLVGEGEIEIEVDGETKTIGVERIHVEQDAGKLMHDQH-- 147
                                               66.6************************************************************976.. PP

                                 TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209
                                               ++ s+vD+NRsgv L+EiV+kPd++s+ ea a+l+klr+ilry++  dg++++GsmR+DvNvs+r +  
  lcl|FitnessBrowser__Korea:Ga0059261_0083 148 PRLSYVDLNRSGVALMEIVSKPDMRSPAEAGAYLSKLRSILRYVGSCDGNMDQGSMRADVNVSVR-RPG 215
                                               68***************************************************************.556 PP

                                 TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278
                                               e++gtr E KN+ns++ + + +e E  Rq++++++g +++qetr fd  k  t s+R+Ke+++DYRYfp
  lcl|FitnessBrowser__Korea:Ga0059261_0083 216 EAFGTRTETKNVNSVRFVMQTVEIEALRQIDVIESGGKIVQETRLFDPDKGETRSMRSKEDAHDYRYFP 284
                                               78******************************************************************* PP

                                 TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepkl 347
                                               +Pdl p+e+d+ +++e  ++ lpelP+akr+r+   +g+  + a vl++++e +++f+ +  + ++  +
  lcl|FitnessBrowser__Korea:Ga0059261_0083 285 DPDLLPLELDDAFLEE-CRGSLPELPDAKRARYL-ALGITPYNAGVLTAEVESARYFDALLDAGAKGPA 351
                                               *************999.***************98.59******************************** PP

                                 TIGR00133 348 avnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklg 416
                                               a+nW+++el g Lnk   +++++ ++p + ael+ l+ +g+is+  ak+++e +le++++p++++e++g
  lcl|FitnessBrowser__Korea:Ga0059261_0083 352 AANWVTSELFGALNKLGKDIENSPVSPAQAAELLGLVADGTISGSLAKQVFEIMLETGGSPSAIVEERG 420
                                               ********************************************************************* PP

                                 TIGR00133 417 liqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkells 481
                                               l q sd+ ++ +++ ev+++np+++e+y+ gke++++f+vGq mk   g+a+p  v++llk+ l+
  lcl|FitnessBrowser__Korea:Ga0059261_0083 421 LKQTSDTGAIEAVIAEVLAKNPGQLEQYRGGKEALFGFFVGQTMKAMGGKANPGVVNELLKKALN 485
                                               **************************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (486 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: 00:00:00.03
# Mc/sec: 7.17
//
[ok]

This GapMind analysis is from Apr 09 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