Alignments for a candidate for glnA in Thioalkalivibrio thiocyanodenitrificans ARhD 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate WP_018232996.1 THITHI_RS0110215 type III glutamate--ammonia ligase

Query= curated2:O27612
         (442 letters)



>NCBI__GCF_000378965.1:WP_018232996.1
          Length = 444

 Score =  306 bits (784), Expect = 9e-88
 Identities = 169/440 (38%), Positives = 263/440 (59%), Gaps = 27/440 (6%)

Query: 17  VKFVRLQFVDIHGKPKNMAIPLVRPDQIEDIIKDGLLFDGSSVEGF-VDINESDLVLKPD 75
           VK++  QFVDIHG  K  ++P+     +ED++ DG  F G +V G  +  +E+D + + D
Sbjct: 15  VKYILAQFVDIHGVAKTKSVPV---SHLEDVLTDGAGFAGFAVWGLRMGPHEADYMARGD 71

Query: 76  PDTFSTLPWRPEEKGVCRFICDIYWPDGKPFEGDPRYVLKRALDKYAHLGYEYNVGPEPE 135
             T S +PW+P   G  R +CD +  +G+P+  D R +L   + +    G+  N G EPE
Sbjct: 72  LGTLSIVPWQP---GYARIVCDGF-VNGEPYMMDTRNILAAQVKRLKERGWTMNTGLEPE 127

Query: 136 FFILDQDEDGNIIPHDCG-----AYFDVEPVDQGTDFRRKLVMDLEALNFDVEVSHHEVA 190
           F +L +D +G ++P D         +D + + +  +F  +LV  L+A++FDV    HE A
Sbjct: 128 FSLLRRDGNGGVVPADDSDRLDKPCYDYKGLSRSREFLERLVESLQAVDFDVYQVDHEDA 187

Query: 191 PGQHEIDFKFDKALKTADAVITFKQAIKAIVDKIGYMVTFMPKPFFGENGSGMHCHQSLF 250
            GQ EI++ +   + +AD  + F+ A   I +++G + +FMPKPF    G+GMH H S+ 
Sbjct: 188 NGQFEINYTYSDCMTSADRYVFFRMAAGEIANQLGLICSFMPKPFSNRTGNGMHMHISIA 247

Query: 251 KD-GENVFYDPDTET--QLSEEALYFIGGLLKHAPALTAVCAPTVNSYKRLVPGYE---- 303
            +   N+F +P       LS+ A +F+ GL++HAPALTA+ AP+VNSYKRLV G      
Sbjct: 248 DETNPNIFEEPSDPRGLSLSKTAYHFMAGLMEHAPALTALMAPSVNSYKRLVVGRALSGA 307

Query: 304 --APVYIAYGLKNRSTLIRIPASRGKGTRVELRMPDPSCNPYLAFAAMLEAGMNGIQNKI 361
             AP +I+YG  NR++++R+P  R     +ELR+ D +CNPYLA AA++ AG++G+  K+
Sbjct: 308 TWAPAFISYGDNNRTSMVRVPQGR-----LELRLGDGACNPYLAAAAVIAAGLDGVDRKL 362

Query: 362 DPGEPTEIDVYEKSMSELREMGIETLPSSLWEAYHALEEDDVIKGALGGHVYEKFMEIKH 421
           +PGEP   + Y+ S +EL E GIETLP SL EA   L +D +    LG    ++F+E+K+
Sbjct: 363 EPGEPQNFNFYDFSPTELAEKGIETLPQSLHEAIETLRKDTLFAEQLGQAFIDEFVELKN 422

Query: 422 REWDDYRVRVFKYELERYLD 441
            EW +Y   V  +EL RY++
Sbjct: 423 MEWVEYSRHVSDWELSRYVE 442


Lambda     K      H
   0.320    0.141    0.433 

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: 532
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: 442
Length of database: 444
Length adjustment: 32
Effective length of query: 410
Effective length of database: 412
Effective search space:   168920
Effective search space used:   168920
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_018232996.1 THITHI_RS0110215 (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.1923829.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-202  657.6   0.0   3.9e-202  657.4   0.0    1.0  1  NCBI__GCF_000378965.1:WP_018232996.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000378965.1:WP_018232996.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  657.4   0.0  3.9e-202  3.9e-202       2     434 ..       7     441 ..       6     442 .. 0.99

  Alignments for each domain:
  == domain 1  score: 657.4 bits;  conditional E-value: 3.9e-202
                             TIGR03105   2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsliqlP 74 
                                           k+ le ++vky+la+fvd++Gvak+k+vPv++l++++++gagfaGfav+gl + P++ad++a +dl +l  +P
  NCBI__GCF_000378965.1:WP_018232996.1   7 KTYLESHDVKYILAQFVDIHGVAKTKSVPVSHLEDVLTDGAGFAGFAVWGLRMGPHEADYMARGDLGTLSIVP 79 
                                           577999******************************************************************* PP

                             TIGR03105  75 wkpevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDkaDklakpc 147
                                           w+p++a++++d++v+g+p+ +++R++l +++++++e+g+t++tG+e+ef+llrr+ +g++++aD++D+l+kpc
  NCBI__GCF_000378965.1:WP_018232996.1  80 WQPGYARIVCDGFVNGEPYMMDTRNILAAQVKRLKERGWTMNTGLEPEFSLLRRDGNGGVVPADDSDRLDKPC 152
                                           ************************************************************************* PP

                             TIGR03105 148 YDqralmrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkylvkeiaeeeglla 220
                                           YD+++l+r++++le+++e+l+++ +d+Yq+DheDanGqfe+n++y+D +t+aDr++ff++++ eia++ gl++
  NCBI__GCF_000378965.1:WP_018232996.1 153 YDYKGLSRSREFLERLVESLQAVDFDVYQVDHEDANGQFEINYTYSDCMTSADRYVFFRMAAGEIANQLGLIC 225
                                           ************************************************************************* PP

                             TIGR03105 221 tfmPkPfadrtGnGlhlhlslldedgknlfaddadeeglglsklayhfiaGilkhakaLaallaPtvnsYkRl 293
                                           +fmPkPf++rtGnG+h+h+s++de+  n+f++++d++gl lsk+ayhf+aG+++ha+aL+al+aP+vnsYkRl
  NCBI__GCF_000378965.1:WP_018232996.1 226 SFMPKPFSNRTGNGMHMHISIADETNPNIFEEPSDPRGLSLSKTAYHFMAGLMEHAPALTALMAPSVNSYKRL 298
                                           ************************************************************************* PP

                             TIGR03105 294 vakrtlsgatWaPalisyggnnRthmvRiPdagRlelRlaDgaanpYlvsaavlaaGLdGierkldpgkrkde 366
                                           v++r+lsgatWaPa+isyg+nnRt mvR+P +gRlelRl+Dga+npYl++aav+aaGLdG++rkl+pg++++ 
  NCBI__GCF_000378965.1:WP_018232996.1 299 VVGRALSGATWAPAFISYGDNNRTSMVRVP-QGRLELRLGDGACNPYLAAAAVIAAGLDGVDRKLEPGEPQNF 370
                                           ******************************.9***************************************** PP

                             TIGR03105 367 nlya...eelaekgvetLPqtLlealraleadelleealGkelveeflklkreeweeyhrtvsdWeidryl 434
                                           n+y+    elaekg+etLPq+L+ea+++l +d+l++e+lG+++++ef++lk++ew+ey+r+vsdWe+ ry+
  NCBI__GCF_000378965.1:WP_018232996.1 371 NFYDfspTELAEKGIETLPQSLHEAIETLRKDTLFAEQLGQAFIDEFVELKNMEWVEYSRHVSDWELSRYV 441
                                           ****9999*************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (444 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.47
//
[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