Alignments for a candidate for gatB in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Rhodospirillum rubrum ATCC 11170

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate YP_428257.1 Rru_A3175 aspartyl/glutamyl-tRNA amidotransferase subunit B

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000013085.1:YP_428257.1
          Length = 485

 Score =  418 bits (1075), Expect = e-121
 Identities = 212/473 (44%), Positives = 314/473 (66%), Gaps = 4/473 (0%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E V+GLEVH ++ + SK+FS S   FGA  NS  +++D A PG+LPV+N   V+ A+R 
Sbjct: 12  WEVVVGLEVHAQVVSQSKLFSGSSTRFGAPANSQVSLVDAAMPGMLPVINGLCVEQAVRT 71

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGITRL 121
            + L  +I   S F RKNYFY D P+ YQISQ++QPI   G + +++ DG ++ +GI RL
Sbjct: 72  GLGLRAKINKRSIFARKNYFYADLPQGYQISQYEQPIVGEGKVVLDMPDGSSREVGIERL 131

Query: 122 HMEEDAGKSTHKGE--YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179
           H+E+DAGKS H      SL+DLNR G  L+EIVS+PD+R P+EA AYL KLRSI++Y G 
Sbjct: 132 HLEQDAGKSMHDQHPTKSLIDLNRSGVALMEIVSKPDMREPEEAGAYLRKLRSIMRYLGT 191

Query: 180 SDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGG 239
            D  MEEGS+R D N+S+RP G     T+ E+KN+NS  +V + +E E  RQ E   SGG
Sbjct: 192 CDGNMEEGSMRADVNVSVRPIGTTDLRTRCEIKNVNSVRFVMQAIEAEAHRQVEVWESGG 251

Query: 240 EIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDER 299
           E+ QETR FD + G+T  MR KE + DYRYFP+PD++PL  DDA+ E+VR+++PELPD++
Sbjct: 252 EVRQETRLFDPAKGETRSMRSKEHAHDYRYFPDPDLLPLEFDDAFVEKVRRSLPELPDDK 311

Query: 300 KAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVEL 359
           K +++ + GL  YDA VL + +E + FFE   E G D K  +NW++  +   L K    +
Sbjct: 312 KNRFIADFGLTPYDASVLVVDRENAAFFEKVAE-GRDGKTAANWVINNLFGALAKAGKGV 370

Query: 360 LDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLL 419
            D+ ++ ENL  ++ L++D  ++ +IAK VF  +   G +   I+ED GL Q++D + + 
Sbjct: 371 ADSPVSAENLGKLLDLLKDEVINGRIAKDVFEIMMETGEDPDAIVEDKGLRQVTDTSAIE 430

Query: 420 KFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
             V+  +  N +  +D + GK K +G+ VGQ+MKA++G+ANP ++N +L+ +L
Sbjct: 431 AAVDAVIAANPEKADDVRGGKEKLLGWFVGQVMKATQGKANPAMLNDILRAKL 483


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: 596
Number of extensions: 30
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: 485
Length adjustment: 34
Effective length of query: 441
Effective length of database: 451
Effective search space:   198891
Effective search space used:   198891
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 YP_428257.1 Rru_A3175 (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.15031.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-166  540.8   0.0   1.5e-166  540.6   0.0    1.0  1  lcl|NCBI__GCF_000013085.1:YP_428257.1  Rru_A3175 aspartyl/glutamyl-tRNA


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013085.1:YP_428257.1  Rru_A3175 aspartyl/glutamyl-tRNA amidotransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.6   0.0  1.5e-166  1.5e-166       3     480 ..      11     483 ..       9     484 .. 0.98

  Alignments for each domain:
  == domain 1  score: 540.6 bits;  conditional E-value: 1.5e-166
                              TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivs 74 
                                             +e+v+GlEvH q+  +sKlF+ +s+++   + N++v+ v+ ++PG lPv+N   v++A+  +l l +ki+ 
  lcl|NCBI__GCF_000013085.1:YP_428257.1  11 TWEVVVGLEVHAQVVSQSKLFSGSSTRFGA-PANSQVSLVDAAMPGMLPVINGLCVEQAVRTGLGLRAKIN- 80 
                                            5799************************99.99************************************66. PP

                              TIGR00133  75 evsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqsl 145
                                            + s+F+RK+YfY DlP+gyqi+q+++Pi+ +Gk+ +++ +++ +e+gierlhlE+D+gks++ ++  ++ sl
  lcl|NCBI__GCF_000013085.1:YP_428257.1  81 KRSIFARKNYFYADLPQGYQISQYEQPIVGEGKVVLDMPDGSsREVGIERLHLEQDAGKSMHDQH--PTKSL 150
                                            69***********************************9887659******************966..78*** PP

                              TIGR00133 146 vDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvE 217
                                            +D+NRsgv L+EiV+kPd+++++ea a+l+klr+i+ryl+  dg++eeGsmR+DvNvs+r+ G+++  tr E
  lcl|NCBI__GCF_000013085.1:YP_428257.1 151 IDLNRSGVALMEIVSKPDMREPEEAGAYLRKLRSIMRYLGTCDGNMEEGSMRADVNVSVRPIGTTDLRTRCE 222
                                            ************************************************************************ PP

                              TIGR00133 218 iKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieide 289
                                            iKN+ns++ + +aie E +Rq++++++g ev qetr fd +k  t s+R+Ke+++DYRYfp+Pdl p+e+d+
  lcl|NCBI__GCF_000013085.1:YP_428257.1 223 IKNVNSVRFVMQAIEAEAHRQVEVWESGGEVRQETRLFDPAKGETRSMRSKEHAHDYRYFPDPDLLPLEFDD 294
                                            ************************************************************************ PP

                              TIGR00133 290 evvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLn 361
                                             +v++ v+  lpelP+ k++r+  ++gl  +da vlv d+e +  fe+v++  +  k+a+nW++++l g L 
  lcl|NCBI__GCF_000013085.1:YP_428257.1 295 AFVEK-VRRSLPELPDDKKNRFIADFGLTPYDASVLVVDRENAAFFEKVAEGRDG-KTAANWVINNLFGALA 364
                                            ***99.*******************************************987776.**************** PP

                              TIGR00133 362 kkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveev 433
                                            k    +a++ +++e+l +l++l+k+++i++++ak+++e ++e+++dp++++e +gl q++d++++ ++v++v
  lcl|NCBI__GCF_000013085.1:YP_428257.1 365 KAGKGVADSPVSAENLGKLLDLLKDEVINGRIAKDVFEIMMETGEDPDAIVEDKGLRQVTDTSAIEAAVDAV 436
                                            ************************************************************************ PP

                              TIGR00133 434 ikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                            i+ np++  + + gkek+l+++vGqvmk t+g+a+p+  + +l+ +l
  lcl|NCBI__GCF_000013085.1:YP_428257.1 437 IAANPEKADDVRGGKEKLLGWFVGQVMKATQGKANPAMLNDILRAKL 483
                                            *****************************************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (485 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: 7.23
//
[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