Alignments for a candidate for glnA in Methanobacterium lacus AL-21

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Methanobacterium lacus AL-21

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha; EC 6.3.1.2 (characterized)
to candidate WP_013646048.1 METBO_RS12305 type I glutamate--ammonia ligase

Query= SwissProt::Q60182
         (454 letters)



>NCBI__GCF_000191585.1:WP_013646048.1
          Length = 442

 Score =  486 bits (1252), Expect = e-142
 Identities = 240/449 (53%), Positives = 316/449 (70%), Gaps = 8/449 (1%)

Query: 5   MEMNVEQAIEYVKKNNVKFIRFQFVDILGFPKNVAYPVKAGEKGIEELREIFENGVWFDG 64
           ME  + + IE +++   KFIR QFVDI G PKN+A P+   E    ++ +I ++G+ FDG
Sbjct: 1   MEDKIGKVIENIERCGTKFIRLQFVDIHGTPKNMAVPISKPE----DIEDILKDGLLFDG 56

Query: 65  SSITGFVGIEESDMLLKPDLSTLSVLPWRPEEKSVARVICDVYKDEKTPFEGDPRSRLKA 124
           SS+ GFV I  SD+++KPD  T S LPWRPEEK V R ICD+Y  + TPFEGDPR  LK 
Sbjct: 57  SSVDGFVDINASDLIIKPDPDTFSTLPWRPEEKGVCRFICDIYWPDMTPFEGDPRYILKK 116

Query: 125 ILEELKKEMNGEYFVGPEPEFFLLKRDPHNPHRWVPADDGGYFDVEPLDDAPDIRRDIVL 184
            L +++ +   EY VGPEPEFF++  D       VP D+G YFDVEP+D   D+RR++VL
Sbjct: 117 ALAKIE-DKGYEYNVGPEPEFFIIGEDAEG--HIVPHDNGIYFDVEPVDQGTDVRRELVL 173

Query: 185 ALENLGFHVEASHHEVAPGQHEVDFKFDNALKTADSVITFKMTIKNIAKKHGLKATFMPK 244
            LE L F VE SHHEV PGQHE+DFKFD+A+KTAD+VITFK  IK I    G   TFMPK
Sbjct: 174 GLEELNFEVEVSHHEVGPGQHEIDFKFDHAMKTADAVITFKQAIKAIVDNLGYMVTFMPK 233

Query: 245 PFFGMNGNGMHCHQSVWFNGEPSFYDPEGPYNGLSETCLSYIAGILSHAKALVAITNPTV 304
           PFFG+NG+GMH HQS++ NG+  FYDP+G  + LSE    +I G+L H+KAL AI  PTV
Sbjct: 234 PFFGVNGSGMHVHQSLFKNGKNIFYDPDGQ-DQLSEEARYFIGGLLKHSKALSAIVAPTV 292

Query: 305 NSYKRLVPGYEAPVNIAWANKNRSAIIRVPAARGKATRIEFRAPDPTCNPYLAFACMLAA 364
           NSYKRLVPGYEAP  IA+  KNRS ++R+PA+RG  TR+EFR PDP+CNPYLAFA ML +
Sbjct: 293 NSYKRLVPGYEAPCYIAYGLKNRSTLVRIPASRGNGTRVEFRCPDPSCNPYLAFAAMLES 352

Query: 365 GLDGIKKKMTAPEPVERNIFKMSEEEKKQLGIESVPANLAAALDELECDEVLQKALGKHI 424
           G+DG+  K+   E  E ++F +     ++ GIE++P++L  A   LE D+V++ +LG H+
Sbjct: 353 GMDGLNNKIDPGEATEIDVFGLDAAGLEREGIETLPSSLWEAYHALEQDDVVKSSLGDHV 412

Query: 425 YENYMEIKRAEWDDFRTAVTDWETGKYLI 453
           Y+ +M+IK+ EWDD+R  V  +E  KYL+
Sbjct: 413 YKQFMDIKKKEWDDYRIQVFPYELEKYLM 441


Lambda     K      H
   0.319    0.137    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: 704
Number of extensions: 34
Number of successful extensions: 5
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: 454
Length of database: 442
Length adjustment: 33
Effective length of query: 421
Effective length of database: 409
Effective search space:   172189
Effective search space used:   172189
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: 51 (24.3 bits)

Align candidate WP_013646048.1 METBO_RS12305 (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.13615.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-186  605.3   0.0   4.8e-143  463.1   0.0    2.0  2  lcl|NCBI__GCF_000191585.1:WP_013646048.1  METBO_RS12305 type I glutamate--


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000191585.1:WP_013646048.1  METBO_RS12305 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.0   1.6e-45   1.6e-45       2     136 ..       7     143 ..       6     147 .. 0.95
   2 !  463.1   0.0  4.8e-143  4.8e-143     163     461 ..     144     440 ..     139     441 .. 0.98

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 1.6e-45
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvsele..eealeegiaFDgssveGfksieesDlllkpd 68 
                                               +v+++++ +  kf++l+fvDi+G++k++++p+s+ e  e++l++g+ FDgssv Gf++i+ sDl++kpd
  lcl|NCBI__GCF_000191585.1:WP_013646048.1   7 KVIENIERCGTKFIRLQFVDIHGTPKNMAVPISKPEdiEDILKDGLLFDGSSVDGFVDINASDLIIKPD 75 
                                               578899999**************************9999****************************** PP

                                 TIGR00653  69 petlvivPfraek..vlrvicdvyepvtkepyerdpRsiakraeeelktklgdevyfGpEaEFflfdkv 135
                                               p+t++++P+r e+  v+r+icd+y+p +++p+e+dpR+i+k+a+ +++ + g+e+++GpE+EFf++ ++
  lcl|NCBI__GCF_000191585.1:WP_013646048.1  76 PDTFSTLPWRPEEkgVCRFICDIYWP-DMTPFEGDPRYILKKALAKIE-DKGYEYNVGPEPEFFIIGED 142
                                               **********99999***********.********************5.99**************9776 PP

                                 TIGR00653 136 e 136
                                                
  lcl|NCBI__GCF_000191585.1:WP_013646048.1 143 A 143
                                               5 PP

  == domain 2  score: 463.1 bits;  conditional E-value: 4.8e-143
                                 TIGR00653 163 nkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvataqaEidikfdklvkaaDeivl 231
                                               + ++ ++++g YfdvepvD+ +d+rrelvl leel++evevsHHEv+++q+Eid+kfd+++k+aD++++
  lcl|NCBI__GCF_000191585.1:WP_013646048.1 144 EGHIVPHDNGIYFDVEPVDQGTDVRRELVLGLEELNFEVEVSHHEVGPGQHEIDFKFDHAMKTADAVIT 212
                                               55678899999********************************************************** PP

                                 TIGR00653 232 yKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHa 300
                                               +K+++k+++++ G+++tFmpKp+fg ngsGmHvh+sl+k+g+n+f++++g+ +Lse+a+y+igG+lkH+
  lcl|NCBI__GCF_000191585.1:WP_013646048.1 213 FKQAIKAIVDNLGYMVTFMPKPFFGVNGSGMHVHQSLFKNGKNIFYDPDGQDQLSEEARYFIGGLLKHS 281
                                               **************************************************999**************** PP

                                 TIGR00653 301 kalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaal 369
                                               kal+A+++ptvnsYkRLvpGyEAP+y+ay+ knRs+l+RiPas+ ++++R+E+R+pDps+npYLafaa+
  lcl|NCBI__GCF_000191585.1:WP_013646048.1 282 KALSAIVAPTVNSYKRLVPGYEAPCYIAYGLKNRSTLVRIPASR-GNGTRVEFRCPDPSCNPYLAFAAM 349
                                               ********************************************.************************ PP

                                 TIGR00653 370 lmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdkevlkevlgeelieafi 438
                                               l  g+dG++nkidpge+++ +++ l+ + l+  Gie+lp+sL+ea+++le+d +v+k+ lg++++++f+
  lcl|NCBI__GCF_000191585.1:WP_013646048.1 350 LESGMDGLNNKIDPGEATEIDVFGLDAAGLEREGIETLPSSLWEAYHALEQD-DVVKSSLGDHVYKQFM 417
                                               ****************************************************.**************** PP

                                 TIGR00653 439 elkrkEveelrlkvhpvElekyl 461
                                               ++k+kE++++r++v+p+Elekyl
  lcl|NCBI__GCF_000191585.1:WP_013646048.1 418 DIKKKEWDDYRIQVFPYELEKYL 440
                                               **********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (442 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 4.36
//
[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