Alignments for a candidate for glnA in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Nitriliruptor alkaliphilus DSM 45188

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_083441797.1 NITAL_RS19560 type I glutamate--ammonia ligase

Query= BRENDA::O85177
         (466 letters)



>NCBI__GCF_000969705.1:WP_083441797.1
          Length = 571

 Score =  629 bits (1622), Expect = 0.0
 Identities = 303/473 (64%), Positives = 356/473 (75%), Gaps = 8/473 (1%)

Query: 2   PTTPDDIQRLIADEDVEVIDVQFCDLPGVMQHFTVPAKAFTEEAYEEGLAFDGSSVRGFQ 61
           P T  D+  LI  E  E +D++F DLPGV QH T P      + +E G+ FDGSSVRGFQ
Sbjct: 99  PQTAQDVLNLIESEGYEFLDLRFIDLPGVTQHTTFPVTNVNADTFENGVYFDGSSVRGFQ 158

Query: 62  SIHESDMLLLPDAATARIDPFRKAKTLALNFFVHDPFTREAYSRDPRNIARKAEQYIAEY 121
            I ESDMLL+PD  TA  D FR  KTLA+   +HDP T EAYSRDPRNIARKAE Y+A  
Sbjct: 159 GIQESDMLLIPDPTTAFEDTFRARKTLAIYCHIHDPVTGEAYSRDPRNIARKAEAYLAST 218

Query: 122 GVADNVYFGPEAEFYIFDSIRFDSAEHASFHEIDSVEGWWNTGADEVGGNQGYKTKFKGG 181
           GVAD  Y GPEAEF+I DS+RFDS  H SF+E+DS+EG WNTG DE GGN+GYK + KGG
Sbjct: 219 GVADTSYMGPEAEFFILDSVRFDSQGHTSFYEVDSIEGSWNTGRDEEGGNKGYKPRQKGG 278

Query: 182 YFPVPPVDHFADLRDDIVRNLQGSGFEIERAHHEVGTAGQTEINYKFNTLLHAADDLQLF 241
           YFPVPP+DH+ DLR ++V NL+  G + +  HHEVG+ GQ EI  +F+TL   AD L  F
Sbjct: 279 YFPVPPMDHYTDLRSEMVHNLEAFGIQTQLHHHEVGSGGQGEIGIQFDTLAKIADKLMTF 338

Query: 242 KYIVKNTVFAAGKTATFMPKPLAGDNGSGMHCHQSLWKDGQPLFHDESGYAGLSDTARHY 301
           KY+VKNT  AAGKT TFMPKP+ GDNGSGMH HQSLWKDG+PLF DESGY  LSDTAR Y
Sbjct: 339 KYVVKNTAAAAGKTVTFMPKPIFGDNGSGMHTHQSLWKDGEPLFFDESGYGQLSDTARWY 398

Query: 302 IGGLLKHAPSLLAFTNPTVNSYHRLVPGFEAPVSLVYSQRNRSACVRIPITGNNPKAKRA 361
           IGGLL+HA S+LAFTNPT NSY RLVPG+EAPV+LVYS RNRSA VRIP++G++PKAKR 
Sbjct: 399 IGGLLEHAKSILAFTNPTTNSYRRLVPGYEAPVNLVYSARNRSAAVRIPMSGDSPKAKRI 458

Query: 362 EFRCPDSSGNPYLAFSAMMMAGLDGIRNKIEPPEPIDKDLYELPPEEAKDVKLVPGDLGT 421
           EFR PD S NPYLAF+AMMMAGLDG+RNKIEP +P+DKD+Y+LPPEE   +  VP  L  
Sbjct: 459 EFRVPDPSSNPYLAFAAMMMAGLDGVRNKIEPADPVDKDIYDLPPEELLGLPSVPRSLEE 518

Query: 422 VLN--------TLEGGVFTPDVIETWISYKRENEIDPLRLRPHPYEFSLYYDV 466
            L          LEGGVFT D+IETWI YK ++E+  + LRPHP+EF LYYD+
Sbjct: 519 ALQGLQDDHEFLLEGGVFTEDLIETWIEYKMDSEVAAVALRPHPHEFELYYDI 571


Lambda     K      H
   0.319    0.138    0.422 

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: 920
Number of extensions: 37
Number of successful extensions: 2
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: 466
Length of database: 571
Length adjustment: 35
Effective length of query: 431
Effective length of database: 536
Effective search space:   231016
Effective search space used:   231016
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_083441797.1 NITAL_RS19560 (type I 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.14208.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-206  671.4   0.0   3.6e-206  671.2   0.0    1.0  1  lcl|NCBI__GCF_000969705.1:WP_083441797.1  NITAL_RS19560 type I glutamate--


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_083441797.1  NITAL_RS19560 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.2   0.0  3.6e-206  3.6e-206       2     462 .]     104     570 ..     103     570 .. 0.99

  Alignments for each domain:
  == domain 1  score: 671.2 bits;  conditional E-value: 3.6e-206
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 
                                               +vl+l++ e  +f+dlrf+D+ G++++ ++pv++++++++e+g+ FDgssv+Gf++i+esD+ll pdp 
  lcl|NCBI__GCF_000969705.1:WP_083441797.1 104 DVLNLIESEGYEFLDLRFIDLPGVTQHTTFPVTNVNADTFENGVYFDGSSVRGFQGIQESDMLLIPDPT 172
                                               67899999************************************************************* PP

                                 TIGR00653  71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138
                                               t++ + fra k+l ++c++++pvt+e y+rdpR+ia++ae +l  t+++d+ y+GpEaEFf++d+v+f+
  lcl|NCBI__GCF_000969705.1:WP_083441797.1 173 TAFEDTFRARKTLAIYCHIHDPVTGEAYSRDPRNIARKAEAYLAsTGVADTSYMGPEAEFFILDSVRFD 241
                                               ********************************************9************************ PP

                                 TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205
                                               ++ ++sf+evds+eg+wn  r++e+gnkgyk+++kggYf+v+p+D+++d+r+e+v++le++g++++ +H
  lcl|NCBI__GCF_000969705.1:WP_083441797.1 242 SQGHTSFYEVDSIEGSWNtgRDEEGGNKGYKPRQKGGYFPVPPMDHYTDLRSEMVHNLEAFGIQTQLHH 310
                                               ******************9999999******************************************** PP

                                 TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273
                                               HEv+++ q Ei+i+fd+l+k aD+++++Kyvvkn+a+  Gkt+tFmpKp+fgdngsGmH+h+slwkdge
  lcl|NCBI__GCF_000969705.1:WP_083441797.1 311 HEVGSGgQGEIGIQFDTLAKIADKLMTFKYVVKNTAAAAGKTVTFMPKPIFGDNGSGMHTHQSLWKDGE 379
                                               ********************************************************************* PP

                                 TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342
                                               +lf +e+gy +Ls+ta++yigG+l+Hak++ A+tnpt+nsY+RLvpGyEAPv+l+ysa+nRsa++RiP+
  lcl|NCBI__GCF_000969705.1:WP_083441797.1 380 PLFFDESGYGQLSDTARWYIGGLLEHAKSILAFTNPTTNSYRRLVPGYEAPVNLVYSARNRSAAVRIPM 448
                                               ********************************************************************* PP

                                 TIGR00653 343 sa.npkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpes 410
                                               s  +pkakRiE+R+pDps+npYLafaa++mAgldG++nki+p +p+dk++y+l++eel   G++++p+s
  lcl|NCBI__GCF_000969705.1:WP_083441797.1 449 SGdSPKAKRIEFRVPDPSSNPYLAFAAMMMAGLDGVRNKIEPADPVDKDIYDLPPEELL--GLPSVPRS 515
                                               **9******************************************************95..6******* PP

                                 TIGR00653 411 Leealdelesdk..evlkevlgeelieafielkr.kEveelrlkvhpvElekyld 462
                                               Leeal+ l+ d+  +++++v++e+lie++ie+k+ +Ev  + l++hp E+e y+d
  lcl|NCBI__GCF_000969705.1:WP_083441797.1 516 LEEALQGLQDDHefLLEGGVFTEDLIETWIEYKMdSEVAAVALRPHPHEFELYYD 570
                                               ************98999*****************99*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (571 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: 9.01
//
[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