Alignments for a candidate for glnA in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Acidovorax sp. GW101-3H11

Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII (uncharacterized)
to candidate Ac3H11_1551 Glutamine synthetase type I (EC 6.3.1.2)

Query= curated2:P31592
         (435 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1551
          Length = 435

 Score =  293 bits (751), Expect = 5e-84
 Identities = 174/414 (42%), Positives = 242/414 (58%), Gaps = 17/414 (4%)

Query: 16  YFMISYTDLFGGQRAKLVPAEAIADMQKDGAGFAGFA-TWLDLTPAHPDLFAVPDASSVI 74
           Y++  + D+ G  +AKLVPA+    +   GAGFAGFA   + + P   +  AV D  S+ 
Sbjct: 6   YYLAQFVDIHGRPKAKLVPAKHKDMIFGAGAGFAGFAIAGMGMGPNGREFMAVGDRDSIR 65

Query: 75  QLPWKKDVAWVAADCVMDDRPVEQAPRVVLKRLVAEAAKE-GLRVKTGVEPEFFLISADG 133
            +PW    A V  +  +D +P    PRV+LK+ +A+  +  GL   TG+EPEFFL+ A  
Sbjct: 66  PVPWMGSTASVTCEGYVDGKPHALDPRVILKKALAKFRETTGLEFFTGLEPEFFLLKAGA 125

Query: 134 S----VISDQFDTAEKPCYDQQAVMRRYDVIAEICDYMLELGWKPYQNDHEDANGQFEMN 189
           +    V++ + ++ +KPCYD + +    D + E+   + E G   YQ DHEDANGQFEMN
Sbjct: 126 AAGSWVVATESESLDKPCYDFRHLSSVSDFLMELRAALEEAGIDVYQIDHEDANGQFEMN 185

Query: 190 WEYDDVLKTADKHSFFKFMVKSVAEKHGLRATFMPKPFKGLTGNGCHAHISVWDVDGRVN 249
           + Y D LKTAD  ++FK   +++A+KHG+  +FMPKPF   +G+G H H+S    +   N
Sbjct: 186 FTYADALKTADNLTYFKMAAQAIAKKHGMLCSFMPKPFAERSGSGLHMHMSAGG-EFCDN 244

Query: 250 AFADK--EMAFGLSAQGKTFLGGIMKHAPALAAITNPTVNSYKRINAPRTTSGATWSPNT 307
           AF DK       LS     FLGG+M +A AL AI  P VNSYKR+    + SGATW+P  
Sbjct: 245 AFEDKTDPREMDLSPMAYQFLGGLMANAAALTAIAAPCVNSYKRLVKSGSRSGATWAPIN 304

Query: 308 VTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLEGIRSQADPGQHYDIDM 367
           + +  NNRT +VRVPG GR ELRLPD A NPYLL A +I AGL+GI  + +PGQ  + ++
Sbjct: 305 IAYGNNNRTALVRVPG-GRLELRLPDAAANPYLLTAAVIYAGLDGIERELEPGQPVNDNL 363

Query: 368 YAEGHLVKDAPR-----LPLNLLDALRAFDADEGLKAAIGAEFSSAYLKLKHLE 416
           Y     V D        LP +L DAL   DA E ++  +G  F + YL +K  E
Sbjct: 364 YVLS--VADLAALGIKCLPTSLPDALDELDASEVMRRGLGEAFIAEYLAVKRAE 415


Lambda     K      H
   0.320    0.135    0.421 

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: 498
Number of extensions: 32
Number of successful extensions: 7
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: 435
Length of database: 435
Length adjustment: 32
Effective length of query: 403
Effective length of database: 403
Effective search space:   162409
Effective search space used:   162409
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate Ac3H11_1551 (Glutamine synthetase type I (EC 6.3.1.2))
to HMM TIGR03105 (glnT: glutamine synthetase, type III (EC 6.3.1.2))

# 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/TIGR03105.hmm
# target sequence database:        /tmp/gapView.6241.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03105  [M=435]
Accession:   TIGR03105
Description: gln_synth_III: glutamine synthetase, type III
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   2.6e-167  542.6   0.0   3.3e-167  542.3   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1551  Glutamine synthetase type I (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1551  Glutamine synthetase type I (EC 6.3.1.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.3   0.0  3.3e-167  3.3e-167      11     435 .]       5     433 ..       2     433 .. 0.98

  Alignments for each domain:
  == domain 1  score: 542.3 bits;  conditional E-value: 3.3e-167
                                        TIGR03105  11 kyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsliq 72 
                                                       y la+fvd++G +kaklvP+++ d++   gagfaGfa+ g+g+ P+  +++av+d ds+ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1551   5 DYYLAQFVDIHGRPKAKLVPAKHKDMIFGAGAGFAGFAIAGMGMGPNGREFMAVGDRDSIRP 66 
                                                      69************************************************************ PP

                                        TIGR03105  73 lPwkpevawvaadlvvegkpvelapRvvlkkllaeaae.kgftlktGveceffllrre.edg 132
                                                      +Pw    a v+++++v+gkp++l+pRv+lkk la+  e +g+++ tG+e+effll++  + g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1551  67 VPWMGSTASVTCEGYVDGKPHALDPRVILKKALAKFREtTGLEFFTGLEPEFFLLKAGaAAG 128
                                                      *********************************9986537***************9862579 PP

                                        TIGR03105 133 klsvaDkaDklakpcYDqralmrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaD 194
                                                      + +va ++++l+kpcYD r l+   d+l e+ +al+e G+d+YqiDheDanGqfe+nf+yaD
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1551 129 SWVVATESESLDKPCYDFRHLSSVSDFLMELRAALEEAGIDVYQIDHEDANGQFEMNFTYAD 190
                                                      99************************************************************ PP

                                        TIGR03105 195 alttaDrvaffkylvkeiaeeegllatfmPkPfadrtGnGlhlhlslldedgknlfaddade 256
                                                      al+taD++++fk++++ ia+++g+l++fmPkPfa+r+G+Glh+h+s   e + n+f+d++d+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1551 191 ALKTADNLTYFKMAAQAIAKKHGMLCSFMPKPFAERSGSGLHMHMSAGGEFCDNAFEDKTDP 252
                                                      ************************************************************** PP

                                        TIGR03105 257 eglglsklayhfiaGilkhakaLaallaPtvnsYkRlvakrtlsgatWaPalisyggnnRth 318
                                                      +++ ls +ay+f++G++++a+aL+a++aP+vnsYkRlv++++ sgatWaP  i+yg+nnRt+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1551 253 REMDLSPMAYQFLGGLMANAAALTAIAAPCVNSYKRLVKSGSRSGATWAPINIAYGNNNRTA 314
                                                      ************************************************************** PP

                                        TIGR03105 319 mvRiPdagRlelRlaDgaanpYlvsaavlaaGLdGierkldpgkrkdenlya...eelaekg 377
                                                      +vR+P +gRlelRl+D+aanpYl++aav+ aGLdGier+l+pg++ ++nly    ++la+ g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1551 315 LVRVP-GGRLELRLPDAAANPYLLTAAVIYAGLDGIERELEPGQPVNDNLYVlsvADLAALG 375
                                                      *****.9********************************************9999999**** PP

                                        TIGR03105 378 vetLPqtLlealraleadelleealGkelveeflklkreeweeyhrtvsdWeidryle 435
                                                      ++ LP++L +al++l+a+e++++ lG+++++e+l +kr e +e   ++s+ e  ry++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1551 376 IKCLPTSLPDALDELDASEVMRRGLGEAFIAEYLAVKRAECDELVLEISKAEFTRYVD 433
                                                      *****************************************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (435 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: 00:00:00.01
# Mc/sec: 12.30
//
[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