GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatB in Pseudomonas fluorescens GW456-L13

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate PfGW456L13_5036 Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7)

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036
          Length = 481

 Score =  455 bits (1171), Expect = e-132
 Identities = 228/481 (47%), Positives = 332/481 (69%), Gaps = 9/481 (1%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +E VIGLE+H +L T SK+FS S   FG+EPN+  +++DL  PGVLPV+N+ AV  A+
Sbjct: 1   MQWEVVIGLEIHTQLTTRSKIFSGSSTTFGSEPNTQASLVDLGMPGVLPVLNQEAVRMAV 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119
              +A++ EI   + F RKNYFYPD PK YQISQ + PI   G++DI + DG  KR+GIT
Sbjct: 61  MFGLAIDAEIGQHNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDIALEDGTVKRVGIT 120

Query: 120 RLHMEEDAGKSTHKGEYSL---VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQY 176
           R H+EEDAGKS H+ E+S    +DLNR GTPL+EIVSEPD+RS KEA AY++ + ++++Y
Sbjct: 121 RAHLEEDAGKSLHE-EFSGATGIDLNRAGTPLLEIVSEPDMRSAKEAVAYVKAIHALVRY 179

Query: 177 TGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELL 236
            G+ D  M EGSLRCD N+S+RP GQ +FGT+ E+KN+NSF ++ K +  E +RQ E + 
Sbjct: 180 LGICDGNMAEGSLRCDCNVSIRPKGQVEFGTRCEIKNVNSFRFIEKAINSEIQRQIELIE 239

Query: 237 SGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELP 296
            GG++ Q+TR +D +  +T  MR KE ++DYRYFP+PD++P+ I++++ + VR T+PELP
Sbjct: 240 DGGKVIQQTRLYDPNKDETRPMRSKEEANDYRYFPDPDLLPVVIENSFLDDVRATLPELP 299

Query: 297 DERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQ 356
            +++ ++  + GL  YDA VL  ++E +D+FE     G D KL +NW+M  +   LNK  
Sbjct: 300 PQKRERFQEQFGLSVYDASVLATSREQADYFEKVASIGGDAKLAANWVMVELGSLLNKQG 359

Query: 357 VELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEA 416
           +++ ++ ++ E L GM+  I+D T+S KIAK VF  +A   G+A +I++  GL Q++D  
Sbjct: 360 LDIEESPVSAELLGGMLLRIKDNTISGKIAKVVFEAMANGEGSADEIIDKRGLKQVTDTG 419

Query: 417 TLLKFVNEALDNNEQSVEDYKNG----KGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
            +   ++E L  N + VE Y+      +GK  GF VGQ MKASKG+ANPQ VN+LLK +L
Sbjct: 420 AISAVLDEMLAANAEQVEQYRAADEAKRGKMFGFFVGQAMKASKGKANPQQVNELLKSKL 479

Query: 473 D 473
           +
Sbjct: 480 E 480


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: 20
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: 481
Length adjustment: 34
Effective length of query: 441
Effective length of database: 447
Effective search space:   197127
Effective search space used:   197127
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 PfGW456L13_5036 (Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7))
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.1162500.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   5.2e-174  565.2   0.0   5.8e-174  565.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036  Aspartyl-tRNA(Asn) amidotransfer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036  Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ 
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.0   0.0  5.8e-174  5.8e-174       2     480 ..       1     479 [.       1     480 [. 0.98

  Alignments for each domain:
  == domain 1  score: 565.0 bits;  conditional E-value: 5.8e-174
                                               TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNke 56 
                                                             +++e+viGlE+H+ql t+sK+F+ +s+ + + +pNt+ + v+lg+PG+lPvlN+e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036   1 MQWEVVIGLEIHTQLTTRSKIFSGSSTTFGS-EPNTQASLVDLGMPGVLPVLNQE 54 
                                                             5789***************************.*********************** PP

                                               TIGR00133  57 avkkAlklalalnskivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleie 111
                                                             av++A++ +la++++i  +  vF+RK+YfYpDlPkgyqi+q +lPi+ +G+l+i 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036  55 AVRMAVMFGLAIDAEIG-QHNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDIA 108
                                                             ***************55.79*********************************** PP

                                               TIGR00133 112 leeke.keigierlhlEeDtgksqykesdkdkqslvDfNRsgvPLlEiVtkPdlk 165
                                                             le++  k++gi+r hlEeD+gks ++e +    + +D+NR+g+PLlEiV++Pd++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 109 LEDGTvKRVGITRAHLEEDAGKSLHEEFS--GATGIDLNRAGTPLLEIVSEPDMR 161
                                                             999888********************775..7999******************** PP

                                               TIGR00133 166 sakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKN 220
                                                             sakea+a++k +++++ryl+i dg++ eGs+R+D+Nvsir+kGq ++gtr EiKN
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 162 SAKEAVAYVKAIHALVRYLGICDGNMAEGSLRCDCNVSIRPKGQVEFGTRCEIKN 216
                                                             ******************************************************* PP

                                               TIGR00133 221 lnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYR 275
                                                             +ns++ iekai+ Ei+Rq++l+++g +v q+tr +d +k  t  +R+Kee++DYR
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 217 VNSFRFIEKAINSEIQRQIELIEDGGKVIQQTRLYDPNKDETRPMRSKEEANDYR 271
                                                             ******************************************************* PP

                                               TIGR00133 276 YfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdle 330
                                                             Yfp+Pdl p++i+++++++ v+++lpelP +kr+r+++++gls +da vl + +e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 272 YFPDPDLLPVVIENSFLDD-VRATLPELPPQKRERFQEQFGLSVYDASVLATSRE 325
                                                             ****************999.*********************************** PP

                                               TIGR00133 331 lldafeevvklikepklavnWileellgeLnkkkislaeallkpeelaeliklik 385
                                                              +d+fe+v++  +++kla+nW++ el + Lnk+ ++++e+ +++e l  ++  ik
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 326 QADYFEKVASIGGDAKLAANWVMVELGSLLNKQGLDIEESPVSAELLGGMLLRIK 380
                                                             ******************************************************* PP

                                               TIGR00133 386 egkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenpke 440
                                                             +++is+k+ak ++e + + +++++++i+k+gl q++d+ ++ ++++e+++ n+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 381 DNTISGKIAKVVFEAMANGEGSADEIIDKRGLKQVTDTGAISAVLDEMLAANAEQ 435
                                                             ******************************************************* PP

                                               TIGR00133 441 vekyk....sgkekalkflvGqvmkktkgradpkevekllkell 480
                                                             ve+y+    +++ k+++f+vGq+mk +kg+a+p++v++llk +l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 436 VEQYRaadeAKRGKMFGFFVGQAMKASKGKANPQQVNELLKSKL 479
                                                             ****9888778899***************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (481 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 33.11
//
[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:

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:

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:

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:

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