Alignments for a candidate for glnA in Methanococcus aeolicus Nankai-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Methanococcus aeolicus Nankai-3

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha; EC 6.3.1.2 (characterized)
to candidate WP_011972874.1 MAEO_RS00755 type I glutamate--ammonia ligase

Query= SwissProt::Q60182
         (454 letters)



>NCBI__GCF_000017185.1:WP_011972874.1
          Length = 448

 Score =  704 bits (1817), Expect = 0.0
 Identities = 332/444 (74%), Positives = 390/444 (87%), Gaps = 1/444 (0%)

Query: 9   VEQAIEYVKKNNVKFIRFQFVDILGFPKNVAYPVKAGEKGIEELREIFENGVWFDGSSIT 68
           ++QA+EY+  N+VKF+R QFVD++G PKNVAYP+K   KG++EL++  ENG++FDGSSI 
Sbjct: 4   IDQAVEYIVSNDVKFLRMQFVDLMGNPKNVAYPIKTDAKGLDELKDTLENGMFFDGSSIE 63

Query: 69  GFVGIEESDMLLKPDLSTLSVLPWRPEEKSVARVICDVYKDEKTPFEGDPRSRLKAILEE 128
           GFVGI ESDM+LKPDLSTLSVLPWRP EKSVARVICDVYK    PFEGDPR  LK IL +
Sbjct: 64  GFVGINESDMVLKPDLSTLSVLPWRPSEKSVARVICDVYKTNGKPFEGDPRGCLKTILGK 123

Query: 129 LKKEMNGEYFVGPEPEFFLLKRDPHNPHRWVPADDGGYFDVEPLDDAPDIRRDIVLALEN 188
           LK+EMNG Y++GPEPEFFL+K DPHNPH+ +PADDGGYFD+EP+D+A  +RRDIV ALE+
Sbjct: 124 LKEEMNGSYYLGPEPEFFLVKPDPHNPHKMIPADDGGYFDLEPMDEASSVRRDIVFALED 183

Query: 189 LGFHVEASHHEVAPGQHEVDFKFDNALKTADSVITFKMTIKNIAKKHGLKATFMPKPFFG 248
           LG+H+EASHHEVA GQ EV+F+F++ALKTAD+VITFK T+K IA++HGL ATFMPKPFFG
Sbjct: 184 LGYHMEASHHEVAEGQSEVNFRFEDALKTADNVITFKTTVKMIAQQHGLTATFMPKPFFG 243

Query: 249 MNGNGMHCHQSVWFNGEPSFYDPEGPYNGLSETCLSYIAGILSHAKALVAITNPTVNSYK 308
           +NG+GMHC+QSVWFN E SFYD   PY  LSET LSYIAGIL +A+ALVAITNPTVNSYK
Sbjct: 244 INGSGMHCNQSVWFNDEVSFYDETAPYQ-LSETALSYIAGILDNARALVAITNPTVNSYK 302

Query: 309 RLVPGYEAPVNIAWANKNRSAIIRVPAARGKATRIEFRAPDPTCNPYLAFACMLAAGLDG 368
           RLVPGYEAPVNIAWAN NRSAIIRVPAARGK TR+EFRAPDPTCNPYLAF  MLAAGLDG
Sbjct: 303 RLVPGYEAPVNIAWANSNRSAIIRVPAARGKGTRVEFRAPDPTCNPYLAFTVMLAAGLDG 362

Query: 369 IKKKMTAPEPVERNIFKMSEEEKKQLGIESVPANLAAALDELECDEVLQKALGKHIYENY 428
           +KK M+AP+PVE NIFKMSE  KK+LGI SVPANL+ ALDELE + +L++ALGKHI+EN+
Sbjct: 363 VKKGMSAPDPVEENIFKMSEARKKELGIASVPANLSEALDELENNSILKEALGKHIFENF 422

Query: 429 MEIKRAEWDDFRTAVTDWETGKYL 452
           +E+KRAEWDDFRT+VTDWET  YL
Sbjct: 423 IELKRAEWDDFRTSVTDWETKTYL 446


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: 737
Number of extensions: 21
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: 454
Length of database: 448
Length adjustment: 33
Effective length of query: 421
Effective length of database: 415
Effective search space:   174715
Effective search space used:   174715
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_011972874.1 MAEO_RS00755 (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.22829.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.9e-185  600.9   0.0   5.5e-183  594.8   0.0    2.0  1  lcl|NCBI__GCF_000017185.1:WP_011972874.1  MAEO_RS00755 type I glutamate--a


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017185.1:WP_011972874.1  MAEO_RS00755 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  594.8   0.0  5.5e-183  5.5e-183       2     461 ..       6     446 ..       5     447 .. 0.97

  Alignments for each domain:
  == domain 1  score: 594.8 bits;  conditional E-value: 5.5e-183
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvsele......eealeegiaFDgssveGfksieesDll 64 
                                               ++++++  ++vkf++++fvD+ G +k+v++p+++        +++le+g+ FDgss+eGf++i+esD++
  lcl|NCBI__GCF_000017185.1:WP_011972874.1   6 QAVEYIVSNDVKFLRMQFVDLMGNPKNVAYPIKTDAkgldelKDTLENGMFFDGSSIEGFVGINESDMV 74 
                                               567788899**********************997666777899************************** PP

                                 TIGR00653  65 lkpdpetlvivPfraek..vlrvicdvyepvtkepyerdpRsiakraeeelktklgdevyfGpEaEFfl 131
                                               lkpd++tl+++P+r ++  v+rvicdvy++ +++p+e+dpR  +k+++ +lk++++ ++y+GpE+EFfl
  lcl|NCBI__GCF_000017185.1:WP_011972874.1  75 LKPDLSTLSVLPWRPSEksVARVICDVYKT-NGKPFEGDPRGCLKTILGKLKEEMNGSYYLGPEPEFFL 142
                                               *************988778**********7.************************************** PP

                                 TIGR00653 132 fdkvefkeasnssflevdseegewnreveegnkgykikkkggYfdvepvDkakdirrelvlaleelgle 200
                                                + + ++ +                        ++ ++++ggYfd+ep+D+a  +rr++v ale+lg +
  lcl|NCBI__GCF_000017185.1:WP_011972874.1 143 VKPDPHNPH------------------------KMIPADDGGYFDLEPMDEASSVRRDIVFALEDLGYH 187
                                               ***999965........................7899******************************** PP

                                 TIGR00653 201 vevsHHEvataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslw 269
                                               +e+sHHEva++q+E++++f++++k+aD+++++K +vk++a++hG+tatFmpKp+fg ngsGmH+++s+w
  lcl|NCBI__GCF_000017185.1:WP_011972874.1 188 MEASHHEVAEGQSEVNFRFEDALKTADNVITFKTTVKMIAQQHGLTATFMPKPFFGINGSGMHCNQSVW 256
                                               ********************************************************************* PP

                                 TIGR00653 270 kdgenlfageeg.yagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsal 337
                                                + e  f++e++ y+ Lsetal yi+Gil  a+al+A+tnptvnsYkRLvpGyEAPv++a++++nRsa+
  lcl|NCBI__GCF_000017185.1:WP_011972874.1 257 FNDEVSFYDETApYQ-LSETALSYIAGILDNARALVAITNPTVNSYKRLVPGYEAPVNIAWANSNRSAI 324
                                               ************777.***************************************************** PP

                                 TIGR00653 338 iRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieq 406
                                               iR+Pa++ +k++R+E+R+pDp++npYLaf+++l+AgldG+k+ + +++p+++n++++se+++kelGi +
  lcl|NCBI__GCF_000017185.1:WP_011972874.1 325 IRVPAAR-GKGTRVEFRAPDPTCNPYLAFTVMLAAGLDGVKKGMSAPDPVEENIFKMSEARKKELGIAS 392
                                               *******.************************************************************* PP

                                 TIGR00653 407 lpesLeealdelesdkevlkevlgeelieafielkrkEveelrlkvhpvElekyl 461
                                               +p++L+ealdele++  +lke+lg++++e+fielkr+E++++r++v+++E+++yl
  lcl|NCBI__GCF_000017185.1:WP_011972874.1 393 VPANLSEALDELENN-SILKEALGKHIFENFIELKRAEWDDFRTSVTDWETKTYL 446
                                               ***************.*************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (448 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 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 4.35
//
[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