Alignments for a candidate for glnA in Rhizobium leguminosarum bv. trifolii WSM1325

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Rhizobium leguminosarum bv. trifolii WSM1325

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII; EC 6.3.1.2 (characterized)
to candidate WP_012763164.1 RLEG_RS26825 type III glutamate--ammonia ligase

Query= SwissProt::O87393
         (435 letters)



>NCBI__GCF_000023185.1:WP_012763164.1
          Length = 435

 Score =  795 bits (2054), Expect = 0.0
 Identities = 375/435 (86%), Positives = 407/435 (93%)

Query: 1   MTLDLSTFAREKGVKYFMISYTDLFGGQRAKLVPAEAIADMQKGGAGFAGFATWFDLTPA 60
           MTLDL+ FA++KG+KYFMISYTDLFGGQRAKLVPAEAIADMQK GAGFAGFATW DLTPA
Sbjct: 1   MTLDLAAFAKDKGIKYFMISYTDLFGGQRAKLVPAEAIADMQKDGAGFAGFATWLDLTPA 60

Query: 61  HPDLFALPDASAVIQLPWKKDVAWVAADCIMDDAPVEQAPRVVLKKLVAEAAQEGLRVKT 120
           HPDLFALPDAS+VIQLPWKKDVAWVAADC+M+D PVEQAPRVVLK+LVAEAA+EGLRVKT
Sbjct: 61  HPDLFALPDASSVIQLPWKKDVAWVAADCVMNDQPVEQAPRVVLKRLVAEAAKEGLRVKT 120

Query: 121 GVEPEFFLISPDGSKISDTFDTAEKPCYDQQAIMRRYDVIAEICDYMLELGWKPYQNDHE 180
           GVEPEFFLIS DGS ISD FDTAEKPCYDQQA+MRRYDVIAEICDYMLELGWKPYQNDHE
Sbjct: 121 GVEPEFFLISADGSVISDQFDTAEKPCYDQQAVMRRYDVIAEICDYMLELGWKPYQNDHE 180

Query: 181 DANGQFEMNWEYDDALRTADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHIS 240
           DANGQFEMNWEYDDAL+TADKHSFFKFMVKS+AEKHGLRATFMPKPFKGLTGNGCH HIS
Sbjct: 181 DANGQFEMNWEYDDALQTADKHSFFKFMVKSVAEKHGLRATFMPKPFKGLTGNGCHAHIS 240

Query: 241 VWDLAGEVNAFADNKAEFGLSAEGRHFLGGIMKHASALAAVTNPTVNSYKRINAPRTISG 300
           VWD+ G+VNAFAD +  FGLSA+G+ FLGGIMKHASALAA+TNPTVNSYKRINAPRT SG
Sbjct: 241 VWDIDGKVNAFADKEMAFGLSAQGKTFLGGIMKHASALAAITNPTVNSYKRINAPRTTSG 300

Query: 301 ATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGVRSKADPG 360
           ATWAPN+VTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGL G+RS+ADPG
Sbjct: 301 ATWAPNTVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLDGIRSQADPG 360

Query: 361 RHYDIDMYKDGHKVTDAPKLPLNLLDALREYNRDEELQEALGREFSAAYLKLKQGEWNTY 420
           RHYDIDMY +G+ V DAP+LPLNLLDALR Y+ DE L++A+G EFSAAYLKLK  EWN +
Sbjct: 361 RHYDIDMYAEGYLVKDAPRLPLNLLDALRAYDADEGLKQAIGAEFSAAYLKLKHQEWNAF 420

Query: 421 CSQFTEWEHQTTLDV 435
           CS FT+WE  +TLD+
Sbjct: 421 CSHFTQWERDSTLDI 435


Lambda     K      H
   0.319    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: 794
Number of extensions: 29
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: 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 WP_012763164.1 RLEG_RS26825 (type III glutamate--ammonia ligase)
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.3812356.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-213  694.0   0.1   3.4e-213  693.9   0.1    1.0  1  NCBI__GCF_000023185.1:WP_012763164.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000023185.1:WP_012763164.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  693.9   0.1  3.4e-213  3.4e-213       2     435 .]       6     434 ..       5     434 .. 0.99

  Alignments for each domain:
  == domain 1  score: 693.9 bits;  conditional E-value: 3.4e-213
                             TIGR03105   2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsliqlP 74 
                                           ++++++kg+ky++++++dl+G ++aklvP+ea+++++k+gagfaGfa++ l+l+Pa++dl+a+pd++s+iqlP
  NCBI__GCF_000023185.1:WP_012763164.1   6 AAFAKDKGIKYFMISYTDLFGGQRAKLVPAEAIADMQKDGAGFAGFATW-LDLTPAHPDLFALPDASSVIQLP 77 
                                           6799*********************************************.*********************** PP

                             TIGR03105  75 wkpevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDkaDklakpc 147
                                           wk++vawvaad+v++++pve+apRvvlk+l+aeaa++g+++ktGve+effl++++   +++++D+ D+++kpc
  NCBI__GCF_000023185.1:WP_012763164.1  78 WKKDVAWVAADCVMNDQPVEQAPRVVLKRLVAEAAKEGLRVKTGVEPEFFLISAD---GSVISDQFDTAEKPC 147
                                           *****************************************************99...789************ PP

                             TIGR03105 148 YDqralmrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkylvkeiaeeeglla 220
                                           YDq+a+mrrydv++ei++++ elGw++Yq+DheDanGqfe+n+ey+Dal+taD+++ffk++vk++ae++gl+a
  NCBI__GCF_000023185.1:WP_012763164.1 148 YDQQAVMRRYDVIAEICDYMLELGWKPYQNDHEDANGQFEMNWEYDDALQTADKHSFFKFMVKSVAEKHGLRA 220
                                           ************************************************************************* PP

                             TIGR03105 221 tfmPkPfadrtGnGlhlhlslldedg.knlfaddadeeglglsklayhfiaGilkhakaLaallaPtvnsYkR 292
                                           tfmPkPf+ +tGnG+h+h+s++d dg  n+fad+  e+++gls+++++f++Gi+kha+aLaa+++PtvnsYkR
  NCBI__GCF_000023185.1:WP_012763164.1 221 TFMPKPFKGLTGNGCHAHISVWDIDGkVNAFADK--EMAFGLSAQGKTFLGGIMKHASALAAITNPTVNSYKR 291
                                           ***********************99989*****9..************************************* PP

                             TIGR03105 293 lvakrtlsgatWaPalisyggnnRthmvRiPdagRlelRlaDgaanpYlvsaavlaaGLdGierkldpgkrkd 365
                                           ++a+rt+sgatWaP++++++gnnRthmvR+P++gR+elRl+Dga+npYl++a+++aaGLdGi++++dpg+++d
  NCBI__GCF_000023185.1:WP_012763164.1 292 INAPRTTSGATWAPNTVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLDGIRSQADPGRHYD 364
                                           ************************************************************************* PP

                             TIGR03105 366 enlyaeelaekgvetLPqtLlealraleadelleealGkelveeflklkreeweeyhrtvsdWeidryle 435
                                           +++yae+  +k++ +LP +Ll+alra++ade l++a+G+e+++++lklk++ew+++++++++We+d++l+
  NCBI__GCF_000023185.1:WP_012763164.1 365 IDMYAEGYLVKDAPRLPLNLLDALRAYDADEGLKQAIGAEFSAAYLKLKHQEWNAFCSHFTQWERDSTLD 434
                                           ******************************************************************9985 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: 00:00:00.00
# Mc/sec: 24.66
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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