Alignments for a candidate for glnA in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Synechococcus elongatus PCC 7942

Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII (uncharacterized)
to candidate Synpcc7942_2296 Synpcc7942_2296 L-glutamine synthetase

Query= curated2:P31592
         (435 letters)



>FitnessBrowser__SynE:Synpcc7942_2296
          Length = 434

 Score =  539 bits (1388), Expect = e-158
 Identities = 256/430 (59%), Positives = 320/430 (74%)

Query: 5   LAAFARDKSIKYFMISYTDLFGGQRAKLVPAEAIADMQKDGAGFAGFATWLDLTPAHPDL 64
           LAA ARD+ I+YF+I++TDLFG QRAKLVPA +I  M   GAGFAGFA WLDL+PA  D+
Sbjct: 4   LAALARDRGIRYFLIAFTDLFGVQRAKLVPASSIDLMATSGAGFAGFAAWLDLSPADADV 63

Query: 65  FAVPDASSVIQLPWKKDVAWVAADCVMDDRPVEQAPRVVLKRLVAEAAKEGLRVKTGVEP 124
            A+PD  S+ QLPW+ +VAW+ AD  ++D+P+EQAPR VLKR+++ A   G R KTGVE 
Sbjct: 64  LAIPDRDSLFQLPWQPEVAWMPADLYLNDQPLEQAPRWVLKRVLSVAESLGYRPKTGVEC 123

Query: 125 EFFLISADGSVISDQFDTAEKPCYDQQAVMRRYDVIAEICDYMLELGWKPYQNDHEDANG 184
           EFFL+   G  I+D  D   KPCYDQQ++MRRYD+I +I + M ELGW PYQ+DHEDANG
Sbjct: 124 EFFLLDETGDAIADPRDRQAKPCYDQQSLMRRYDLITQISEAMEELGWGPYQSDHEDANG 183

Query: 185 QFEMNWEYDDVLKTADKHSFFKFMVKSVAEKHGLRATFMPKPFKGLTGNGCHAHISVWDV 244
           QFEMNW Y D L TAD+ +FFK+MVK++AE+ GLRATFMPKPF  LTGNGCH H+S+W+ 
Sbjct: 184 QFEMNWTYADALVTADRQAFFKYMVKTLAERQGLRATFMPKPFADLTGNGCHMHLSLWNR 243

Query: 245 DGRVNAFADKEMAFGLSAQGKTFLGGIMKHAPALAAITNPTVNSYKRINAPRTTSGATWS 304
           +G  N F D      LS  G  F+GG++  A +L A+TNPT+NSYKRINAP TTSGATWS
Sbjct: 244 EGTTNTFVDPVATAPLSTLGYQFIGGLLHSAASLCALTNPTINSYKRINAPATTSGATWS 303

Query: 305 PNTVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLEGIRSQADPGQHYD 364
           PN ++++GNNRTH++R+P  GRFELRL DGA NPYLL A  IAAGL+GI+++ DPG  YD
Sbjct: 304 PNGISYSGNNRTHLIRIPDAGRFELRLADGAANPYLLPAAAIAAGLDGIQNKRDPGPRYD 363

Query: 365 IDMYAEGHLVKDAPRLPLNLLDALRAFDADEGLKAAIGAEFSSAYLKLKHLEWNAYCSHF 424
            D YA+       P LP +LLDALR+      L   +GA F+SAYLKLKH EW ++C+  
Sbjct: 364 NDNYAQPLPPGTVPTLPEHLLDALRSLQESTVLTEGLGAAFTSAYLKLKHQEWRSFCAEI 423

Query: 425 TQWERDSTLD 434
           T WER +TLD
Sbjct: 424 TPWERATTLD 433


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: 631
Number of extensions: 27
Number of successful extensions: 1
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: 434
Length adjustment: 32
Effective length of query: 403
Effective length of database: 402
Effective search space:   162006
Effective search space used:   162006
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 Synpcc7942_2296 Synpcc7942_2296 (L-glutamine synthetase)
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.13998.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.6e-212  689.4   0.0   8.6e-212  689.2   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2296  Synpcc7942_2296 L-glutamine synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2296  Synpcc7942_2296 L-glutamine synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.2   0.0  8.6e-212  8.6e-212       2     435 .]       5     433 ..       4     433 .. 0.99

  Alignments for each domain:
  == domain 1  score: 689.2 bits;  conditional E-value: 8.6e-212
                                 TIGR03105   2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsl 70 
                                               ++l++++g++y+l+af+dl+Gv++aklvP++++d +a++gagfaGfa++ l+l+Padad+la+pd dsl
  lcl|FitnessBrowser__SynE:Synpcc7942_2296   5 AALARDRGIRYFLIAFTDLFGVQRAKLVPASSIDLMATSGAGFAGFAAW-LDLSPADADVLAIPDRDSL 72 
                                               6899*********************************************.******************* PP

                                 TIGR03105  71 iqlPwkpevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDk 139
                                               +qlPw+pevaw++adl+++++p+e+apR+vlk++l+ a++ g++ ktGveceffll+++   + ++aD 
  lcl|FitnessBrowser__SynE:Synpcc7942_2296  73 FQLPWQPEVAWMPADLYLNDQPLEQAPRWVLKRVLSVAESLGYRPKTGVECEFFLLDET---GDAIADP 138
                                               **********************************************************9...778**** PP

                                 TIGR03105 140 aDklakpcYDqralmrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkyl 208
                                               +D++akpcYDq++lmrryd++++isea++elGw++Yq+DheDanGqfe+n++yaDal+taDr+affky+
  lcl|FitnessBrowser__SynE:Synpcc7942_2296 139 RDRQAKPCYDQQSLMRRYDLITQISEAMEELGWGPYQSDHEDANGQFEMNWTYADALVTADRQAFFKYM 207
                                               ********************************************************************* PP

                                 TIGR03105 209 vkeiaeeegllatfmPkPfadrtGnGlhlhlslldedg.knlfaddadeeglglsklayhfiaGilkha 276
                                               vk++ae++gl+atfmPkPfad+tGnG+h+hlsl++++g +n+f d+   ++ +ls+l+y+fi+G+l++a
  lcl|FitnessBrowser__SynE:Synpcc7942_2296 208 VKTLAERQGLRATFMPKPFADLTGNGCHMHLSLWNREGtTNTFVDP--VATAPLSTLGYQFIGGLLHSA 274
                                               ***********************************99989******..999****************** PP

                                 TIGR03105 277 kaLaallaPtvnsYkRlvakrtlsgatWaPalisyggnnRthmvRiPdagRlelRlaDgaanpYlvsaa 345
                                               ++L+al++Pt+nsYkR++a++t+sgatW+P+ isy+gnnRth++RiPdagR+elRlaDgaanpYl+ aa
  lcl|FitnessBrowser__SynE:Synpcc7942_2296 275 ASLCALTNPTINSYKRINAPATTSGATWSPNGISYSGNNRTHLIRIPDAGRFELRLADGAANPYLLPAA 343
                                               ********************************************************************* PP

                                 TIGR03105 346 vlaaGLdGierkldpgkrkdenlyaeelaekgvetLPqtLlealraleadelleealGkelveeflklk 414
                                               ++aaGLdGi++k+dpg+r+d+++ya++l   +v tLP++Ll+alr+l+++++l+e lG+++++++lklk
  lcl|FitnessBrowser__SynE:Synpcc7942_2296 344 AIAAGLDGIQNKRDPGPRYDNDNYAQPLPPGTVPTLPEHLLDALRSLQESTVLTEGLGAAFTSAYLKLK 412
                                               ********************************************************************* PP

                                 TIGR03105 415 reeweeyhrtvsdWeidryle 435
                                               ++ew+++++++++We+ ++l+
  lcl|FitnessBrowser__SynE:Synpcc7942_2296 413 HQEWRSFCAEITPWERATTLD 433
                                               ****************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (434 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.12
//
[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