Alignments for a candidate for glnA in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Methanococcus maripaludis C5

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha; EC 6.3.1.2 (characterized)
to candidate WP_011868155.1 MMARC5_RS01960 type I glutamate--ammonia ligase

Query= SwissProt::Q60182
         (454 letters)



>NCBI__GCF_000016125.1:WP_011868155.1
          Length = 446

 Score =  681 bits (1757), Expect = 0.0
 Identities = 329/445 (73%), Positives = 375/445 (84%), Gaps = 3/445 (0%)

Query: 8   NVEQAIEYVKKNNVKFIRFQFVDILGFPKNVAYPVKAGEKGIEELREIFENGVWFDGSSI 67
           +VEQA++Y+K NNVKFIRFQFVDI G PKN+AYPVKAG  G EEL ++ E G++FDGSSI
Sbjct: 3   SVEQAMDYIKTNNVKFIRFQFVDIHGEPKNIAYPVKAGAAGEEELYDVLEKGLYFDGSSI 62

Query: 68  TGFVGIEESDMLLKPDLSTLSVLPWRPEEKSVARVICDVYKDEKTPFEGDPRSRLKAILE 127
            GFV IE SDM+LKPDL TLSVLPWRP EKSVARVICDVY     PFEGDPR  LK +L 
Sbjct: 63  EGFVSIESSDMMLKPDLKTLSVLPWRPTEKSVARVICDVYTTTGKPFEGDPRGCLKRVLA 122

Query: 128 ELKKEMNGEYFVGPEPEFFLLKRDPHNPHRWVPADDGGYFDVEPLDDAPDIRRDIVLALE 187
           +  +E+ GE+FVGPEPEFF+LK D      WVPADD GYFD+EPLD   DIRR IV ALE
Sbjct: 123 KFDEELGGEFFVGPEPEFFILKEDACGS--WVPADDAGYFDLEPLDGGCDIRRKIVFALE 180

Query: 188 NLGFHVEASHHEVAPGQHEVDFKFDNALKTADSVITFKMTIKNIAKKHGLKATFMPKPFF 247
           NLGFHVEASHHEVA GQHEVDFKF +A+KTADSV+TFK TIK +A + GLKATFMPKPFF
Sbjct: 181 NLGFHVEASHHEVAEGQHEVDFKFADAVKTADSVVTFKTTIKTLAAQEGLKATFMPKPFF 240

Query: 248 GMNGNGMHCHQSVWFNGEPSFYDPEGPYNGLSETCLSYIAGILSHAKALVAITNPTVNSY 307
           G+NG+GMHCHQS+W NGEPSFYD    Y  LSETC+SY+AGIL HAK++VA+TNPTVNSY
Sbjct: 241 GINGSGMHCHQSIWLNGEPSFYDESAQYQ-LSETCMSYVAGILDHAKSIVAVTNPTVNSY 299

Query: 308 KRLVPGYEAPVNIAWANKNRSAIIRVPAARGKATRIEFRAPDPTCNPYLAFACMLAAGLD 367
           KRLVPGYEAPVNIAWAN NRSAI+RVPA RGK TRIEFRAPDP+CNPYLAF  MLAAGLD
Sbjct: 300 KRLVPGYEAPVNIAWANANRSAIVRVPAPRGKGTRIEFRAPDPSCNPYLAFTVMLAAGLD 359

Query: 368 GIKKKMTAPEPVERNIFKMSEEEKKQLGIESVPANLAAALDELECDEVLQKALGKHIYEN 427
           G+K+K++A +PVE+NIF MSE +KK  GIESVPANL AALDELE + VL+ ALGKHI+EN
Sbjct: 360 GVKRKLSAIDPVEKNIFAMSEAQKKAEGIESVPANLKAALDELENNSVLKDALGKHIFEN 419

Query: 428 YMEIKRAEWDDFRTAVTDWETGKYL 452
           ++EIK AEWD FRT+VTDWET +YL
Sbjct: 420 FIEIKNAEWDSFRTSVTDWETKQYL 444


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: 697
Number of extensions: 19
Number of successful extensions: 3
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: 446
Length adjustment: 33
Effective length of query: 421
Effective length of database: 413
Effective search space:   173873
Effective search space used:   173873
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_011868155.1 MMARC5_RS01960 (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.23105.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-186  605.6   0.0   6.8e-184  597.8   0.0    2.0  1  lcl|NCBI__GCF_000016125.1:WP_011868155.1  MMARC5_RS01960 type I glutamate-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016125.1:WP_011868155.1  MMARC5_RS01960 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  597.8   0.0  6.8e-184  6.8e-184       1     461 [.       5     444 ..       5     445 .. 0.98

  Alignments for each domain:
  == domain 1  score: 597.8 bits;  conditional E-value: 6.8e-184
                                 TIGR00653   1 eevlkllkeenvkfvdlrfvDikGklkkveipvsele......eealeegiaFDgssveGfksieesDl 63 
                                               e++++++k +nvkf++++fvDi+G +k++++pv++         ++le+g+ FDgss+eGf+sie sD+
  lcl|NCBI__GCF_000016125.1:WP_011868155.1   5 EQAMDYIKTNNVKFIRFQFVDIHGEPKNIAYPVKAGAageeelYDVLEKGLYFDGSSIEGFVSIESSDM 73 
                                               578899***************************9987777766789*********************** PP

                                 TIGR00653  64 llkpdpetlvivPfraek..vlrvicdvyepvtkepyerdpRsiakraeeelktklgdevyfGpEaEFf 130
                                               +lkpd++tl+++P+r ++  v+rvicdvy++ t++p+e+dpR  +kr++ ++ ++lg e+++GpE+EFf
  lcl|NCBI__GCF_000016125.1:WP_011868155.1  74 MLKPDLKTLSVLPWRPTEksVARVICDVYTT-TGKPFEGDPRGCLKRVLAKFDEELGGEFFVGPEPEFF 141
                                               **************988778**********7.************************************* PP

                                 TIGR00653 131 lfdkvefkeasnssflevdseegewnreveegnkgykikkkggYfdvepvDkakdirrelvlaleelgl 199
                                               +++++  +                          ++ ++++ gYfd+ep+D   dirr++v ale+lg+
  lcl|NCBI__GCF_000016125.1:WP_011868155.1 142 ILKEDACG--------------------------SWVPADDAGYFDLEPLDGGCDIRRKIVFALENLGF 184
                                               ****9998..........................5799******************************* PP

                                 TIGR00653 200 evevsHHEvataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlsl 268
                                               +ve+sHHEva++q+E+d+kf+++vk+aD++v++K ++k++a+++G++atFmpKp+fg ngsGmH+h+s+
  lcl|NCBI__GCF_000016125.1:WP_011868155.1 185 HVEASHHEVAEGQHEVDFKFADAVKTADSVVTFKTTIKTLAAQEGLKATFMPKPFFGINGSGMHCHQSI 253
                                               ********************************************************************* PP

                                 TIGR00653 269 wkdgenlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsal 337
                                               w +ge+ f++e+++ +Lset++ y++Gil Hak+++A+tnptvnsYkRLvpGyEAPv++a+++ nRsa+
  lcl|NCBI__GCF_000016125.1:WP_011868155.1 254 WLNGEPSFYDESAQYQLSETCMSYVAGILDHAKSIVAVTNPTVNSYKRLVPGYEAPVNIAWANANRSAI 322
                                               *************666***************************************************** PP

                                 TIGR00653 338 iRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieq 406
                                               +R+Pa + +k++RiE+R+pDps+npYLaf+++l+AgldG+k+k+ + +p++kn++ +se+++k  Gie+
  lcl|NCBI__GCF_000016125.1:WP_011868155.1 323 VRVPAPR-GKGTRIEFRAPDPSCNPYLAFTVMLAAGLDGVKRKLSAIDPVEKNIFAMSEAQKKAEGIES 390
                                               *******.************************************************************* PP

                                 TIGR00653 407 lpesLeealdelesdkevlkevlgeelieafielkrkEveelrlkvhpvElekyl 461
                                               +p++L++aldele++  vlk++lg++++e+fie+k++E++++r++v+++E+++yl
  lcl|NCBI__GCF_000016125.1:WP_011868155.1 391 VPANLKAALDELENN-SVLKDALGKHIFENFIEIKNAEWDSFRTSVTDWETKQYL 444
                                               ***************.**************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (446 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: 4.18
//
[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