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 glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate WP_018233065.1 THITHI_RS0110580 glutamate--ammonia ligase

Query= CharProtDB::CH_024014
         (469 letters)



>NCBI__GCF_000378965.1:WP_018233065.1
          Length = 469

 Score =  702 bits (1811), Expect = 0.0
 Identities = 331/469 (70%), Positives = 393/469 (83%)

Query: 1   MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60
           MS   V+  + E+ VKFVD RFTD++GKEQHV++PAH +  + FE GKMFDGSSI GWKG
Sbjct: 1   MSPAEVIKTIKENGVKFVDFRFTDSRGKEQHVSVPAHSIEEDTFESGKMFDGSSIAGWKG 60

Query: 61  INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTG 120
           INESDM+LMPD ++AV+DPFF + TL +RCD++EP T+QGYDR PRS+A+RAE YL STG
Sbjct: 61  INESDMILMPDPASAVMDPFFDEPTLNLRCDVVEPATMQGYDRCPRSLARRAEAYLASTG 120

Query: 121 IADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGY 180
           IADT LFGPE EFF+FDD+++G+ ISG    +D  E +WNS   +EGGN GHRP VKGGY
Sbjct: 121 IADTALFGPENEFFVFDDVKWGNEISGCFFRVDSDEASWNSEKVFEGGNIGHRPTVKGGY 180

Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240
           FPVPPVDS QD+RS MCL +E+MGL  E HHHEVATAGQ E+     T+T+KADE+QI K
Sbjct: 181 FPVPPVDSLQDLRSAMCLGLEEMGLTTEVHHHEVATAGQCEIGVGAATLTRKADEVQILK 240

Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIG 300
           YVV NVAH +GKTATFMPKP+ GDNGSGMH HMSLS++GVNLF+GD+Y GLSE ALYYIG
Sbjct: 241 YVVQNVAHNYGKTATFMPKPLVGDNGSGMHVHMSLSRDGVNLFSGDQYGGLSEMALYYIG 300

Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVR 360
           GVIKHA+A+NA  N +TNSYKRLVPG+EAPVMLAYSARNRSASIRIP V +PK RRIEVR
Sbjct: 301 GVIKHARALNAFTNASTNSYKRLVPGFEAPVMLAYSARNRSASIRIPFVMNPKGRRIEVR 360

Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420
           FPD  ANPYL FAA++MAGLDGI+NKIHPGEAMDKNLYDLPPEE K+IPQV  +L++AL+
Sbjct: 361 FPDSTANPYLAFAAMMMAGLDGIQNKIHPGEAMDKNLYDLPPEEEKQIPQVCHALDQALD 420

Query: 421 ELDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469
            LD DR FLKAGGVFTD+ IDAYI+L+ E+  R+RMT HPVE++LYYS+
Sbjct: 421 ALDKDRTFLKAGGVFTDDMIDAYISLKMEDVTRMRMTTHPVEYDLYYSL 469


Lambda     K      H
   0.318    0.136    0.400 

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: 750
Number of extensions: 19
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: 469
Length adjustment: 33
Effective length of query: 436
Effective length of database: 436
Effective search space:   190096
Effective search space used:   190096
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_018233065.1 THITHI_RS0110580 (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.9733.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-206  672.9   0.0   1.2e-206  672.8   0.0    1.0  1  lcl|NCBI__GCF_000378965.1:WP_018233065.1  THITHI_RS0110580 glutamate--ammo


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000378965.1:WP_018233065.1  THITHI_RS0110580 glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  672.8   0.0  1.2e-206  1.2e-206       2     462 .]       5     468 ..       4     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 672.8 bits;  conditional E-value: 1.2e-206
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 
                                               ev+k++ke+ vkfvd+rf+D +Gk+++v++p++++ee+++e+g++FDgss+ G+k+i+esD++l+pdp 
  lcl|NCBI__GCF_000378965.1:WP_018233065.1   5 EVIKTIKENGVKFVDFRFTDSRGKEQHVSVPAHSIEEDTFESGKMFDGSSIAGWKGINESDMILMPDPA 73 
                                               6899***************************************************************** PP

                                 TIGR00653  71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138
                                               ++v++Pf +e++l+++cdv ep+t++ y+r+pRs a+rae +l  t+++d++ fGpE+EFf+fd+v+ +
  lcl|NCBI__GCF_000378965.1:WP_018233065.1  74 SAVMDPFFDEPTLNLRCDVVEPATMQGYDRCPRSLARRAEAYLAsTGIADTALFGPENEFFVFDDVKWG 142
                                               ********************************************9************************ PP

                                 TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205
                                               ++ +  f++vds e++wn  + +e+gn g++++ kggYf+v+pvD+++d+r+ ++l lee+gl++ev+H
  lcl|NCBI__GCF_000378965.1:WP_018233065.1 143 NEISGCFFRVDSDEASWNseKVFEGGNIGHRPTVKGGYFPVPPVDSLQDLRSAMCLGLEEMGLTTEVHH 211
                                               ******************98889999******************************************* PP

                                 TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273
                                               HEvata q Ei++  ++l+++aDe++++Kyvv+nva+++GktatFmpKpl+gdngsGmHvh+sl++dg 
  lcl|NCBI__GCF_000378965.1:WP_018233065.1 212 HEVATAgQCEIGVGAATLTRKADEVQILKYVVQNVAHNYGKTATFMPKPLVGDNGSGMHVHMSLSRDGV 280
                                               ********************************************************************* PP

                                 TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342
                                               nlf+g++ y gLse+alyyigG++kHa+al+A+tn+++nsYkRLvpG+EAPv+laysa+nRsa+iRiP 
  lcl|NCBI__GCF_000378965.1:WP_018233065.1 281 NLFSGDQ-YGGLSEMALYYIGGVIKHARALNAFTNASTNSYKRLVPGFEAPVMLAYSARNRSASIRIPF 348
                                               *******.************************************************************* PP

                                 TIGR00653 343 sanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411
                                               ++npk++RiEvR+pD++anpYLafaa++mAgldGi+nki+pge++dknly+l++ee k+  i+q+ + L
  lcl|NCBI__GCF_000378965.1:WP_018233065.1 349 VMNPKGRRIEVRFPDSTANPYLAFAAMMMAGLDGIQNKIHPGEAMDKNLYDLPPEEEKQ--IPQVCHAL 415
                                               ***********************************************************..******** PP

                                 TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                               ++ald+l++d+  +++++v+++++i+a+i+lk+++v ++r++ hpvE   y++
  lcl|NCBI__GCF_000378965.1:WP_018233065.1 416 DQALDALDKDRtfLKAGGVFTDDMIDAYISLKMEDVTRMRMTTHPVEYDLYYS 468
                                               ***********999999**********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (469 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.41
//
[ok]

This GapMind analysis is from Apr 10 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