Alignments for a candidate for glnA in Thermithiobacillus tepidarius DSM 3134

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Thermithiobacillus tepidarius DSM 3134

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_028989447.1 G579_RS0105900 glutamate--ammonia ligase

Query= BRENDA::P0A1P6
         (469 letters)



>NCBI__GCF_000423825.1:WP_028989447.1
          Length = 471

 Score =  689 bits (1779), Expect = 0.0
 Identities = 329/468 (70%), Positives = 383/468 (81%)

Query: 2   SAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGI 61
           + + V  ++ E++VKF+DLRFTDTKGKEQHV++PAH ++   FEEGK FDGSSI GWK I
Sbjct: 4   AVKDVFKLIEENDVKFIDLRFTDTKGKEQHVSMPAHALDEGAFEEGKAFDGSSIAGWKHI 63

Query: 62  NESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATGI 121
           NESDM+L  D S+AV+DPF  ++TLIIRCDI+EP T +GY+RDPRSIAKRAE YL++TGI
Sbjct: 64  NESDMILKLDPSSAVMDPFMDENTLIIRCDIIEPATGEGYERDPRSIAKRAEAYLKSTGI 123

Query: 122 ADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGYF 181
           ADT  FGPE EFF+FD + +   +SG    ID  E AWNS  +YE GN  HRP VKGGYF
Sbjct: 124 ADTAYFGPENEFFIFDSVTWSIDMSGCSYKIDSQEAAWNSGKEYESGNMAHRPSVKGGYF 183

Query: 182 PVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKY 241
           PVPPVDS+QDIRS MCL +E+MG+ VE HHHEVATA QNE+   F T+T+KADE+QI KY
Sbjct: 184 PVPPVDSSQDIRSAMCLALEEMGIKVEVHHHEVATANQNEIGVAFGTLTRKADEVQILKY 243

Query: 242 VVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIGG 301
           VVHNVAH +G TATFMPKP+ GDNGSGMH HMSLAK+G NLFSGD Y G+SE ALYYIGG
Sbjct: 244 VVHNVAHAYGHTATFMPKPIVGDNGSGMHVHMSLAKDGKNLFSGDGYGGMSELALYYIGG 303

Query: 302 VIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVRF 361
           +IKHAKA+NA+ NP+TNSYKRLVPG+EAPVMLAYSARNRSASIRIP V +PKARRIEVRF
Sbjct: 304 IIKHAKALNAITNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPFVTNPKARRIEVRF 363

Query: 362 PDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNA 421
           PD  ANPYL FAA++MAGLDGI+NKIHPGEAMDK+LYDLP EE K IPQV GSL EAL+A
Sbjct: 364 PDSTANPYLAFAAMMMAGLDGIQNKIHPGEAMDKDLYDLPAEEKKSIPQVCGSLSEALDA 423

Query: 422 LDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469
           LD DR FL  GGVFTD  +DA+I L+R E   V MT HPVE  +YYS+
Sbjct: 424 LDADRAFLTKGGVFTDSMLDAFIELKRAEVQEVNMTTHPVEMRMYYSL 471


Lambda     K      H
   0.318    0.136    0.401 

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: 767
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: 469
Length of database: 471
Length adjustment: 33
Effective length of query: 436
Effective length of database: 438
Effective search space:   190968
Effective search space used:   190968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_028989447.1 G579_RS0105900 (glutamate--ammonia ligase)
to HMM TIGR00653 (glnA: glutamine synthetase, type I (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/TIGR00653.hmm
# target sequence database:        /tmp/gapView.47272.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00653  [M=462]
Accession:   TIGR00653
Description: GlnA: glutamine synthetase, type I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-212  691.4   0.1   3.1e-212  691.2   0.1    1.0  1  NCBI__GCF_000423825.1:WP_028989447.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000423825.1:WP_028989447.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  691.2   0.1  3.1e-212  3.1e-212       2     462 .]       7     470 ..       6     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: 691.2 bits;  conditional E-value: 3.1e-212
                             TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvi 74 
                                           +v+kl++e++vkf+dlrf+D+kGk+++v++p+++l+e a+eeg+aFDgss+ G+k+i+esD++lk dp+++v+
  NCBI__GCF_000423825.1:WP_028989447.1   7 DVFKLIEENDVKFIDLRFTDTKGKEQHVSMPAHALDEGAFEEGKAFDGSSIAGWKHINESDMILKLDPSSAVM 79 
                                           789********************************************************************** PP

                             TIGR00653  75 vPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssfl 146
                                           +Pf++e++l+++cd+ ep+t+e yerdpRsiakrae +lk t+++d++yfGpE+EFf+fd+v+ +  ++   +
  NCBI__GCF_000423825.1:WP_028989447.1  80 DPFMDENTLIIRCDIIEPATGEGYERDPRSIAKRAEAYLKsTGIADTAYFGPENEFFIFDSVTWSIDMSGCSY 152
                                           ************************************************************************* PP

                             TIGR00653 147 evdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEid 216
                                           ++ds+e++wn  +e+e+gn +++++ kggYf+v+pvD+ +dir+ ++lalee+g++vev+HHEvata q+Ei+
  NCBI__GCF_000423825.1:WP_028989447.1 153 KIDSQEAAWNsgKEYESGNMAHRPSVKGGYFPVPPVDSSQDIRSAMCLALEEMGIKVEVHHHEVATAnQNEIG 225
                                           ***********9************************************************************* PP

                             TIGR00653 217 ikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLseta 289
                                           + f +l+++aDe++++Kyvv+nva+ +G+tatFmpKp++gdngsGmHvh+sl kdg+nlf+g+  y g+se a
  NCBI__GCF_000423825.1:WP_028989447.1 226 VAFGTLTRKADEVQILKYVVHNVAHAYGHTATFMPKPIVGDNGSGMHVHMSLAKDGKNLFSGDG-YGGMSELA 297
                                           ***************************************************************9.******** PP

                             TIGR00653 290 lyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanp 362
                                           lyyigGi+kHakal+A+tnp++nsYkRLvpG+EAPv+laysa+nRsa+iRiP ++npka+RiEvR+pD++anp
  NCBI__GCF_000423825.1:WP_028989447.1 298 LYYIGGIIKHAKALNAITNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPFVTNPKARRIEVRFPDSTANP 370
                                           ************************************************************************* PP

                             TIGR00653 363 YLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeel 433
                                           YLafaa++mAgldGi+nki+pge++dk+ly+l+ ee+k+  i+q+  sL+eald+l++d+  +++++v+++ +
  NCBI__GCF_000423825.1:WP_028989447.1 371 YLAFAAMMMAGLDGIQNKIHPGEAMDKDLYDLPAEEKKS--IPQVCGSLSEALDALDADRafLTKGGVFTDSM 441
                                           ***************************************..*******************9999********* PP

                             TIGR00653 434 ieafielkrkEveelrlkvhpvElekyld 462
                                           ++afielkr+Ev+e++++ hpvE+ +y++
  NCBI__GCF_000423825.1:WP_028989447.1 442 LDAFIELKRAEVQEVNMTTHPVEMRMYYS 470
                                           ***************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (471 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: 16.48
//
[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