Alignments for a candidate for glnA in Methylomonas methanica MC09

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Methylomonas methanica MC09

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_013819544.1 METME_RS14745 glutamate--ammonia ligase

Query= BRENDA::P0A1P6
         (469 letters)



>NCBI__GCF_000214665.1:WP_013819544.1
          Length = 469

 Score =  703 bits (1815), Expect = 0.0
 Identities = 333/469 (71%), Positives = 388/469 (82%)

Query: 1   MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60
           MS E+VL M+ E++V+FVD RF DT+GKEQHVT PAH ++ + FEEG MFDGSS+ GWK 
Sbjct: 1   MSVENVLKMIQENDVQFVDFRFCDTRGKEQHVTFPAHTIDEDTFEEGNMFDGSSVAGWKH 60

Query: 61  INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATG 120
           INESDM+LMPD STA IDPFF D T+I+RCDI+EP  +QGY RDPRSIAKRAE Y+++TG
Sbjct: 61  INESDMILMPDPSTAKIDPFFDDKTVILRCDIIEPKDMQGYGRDPRSIAKRAEAYMQSTG 120

Query: 121 IADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGY 180
           IADT  FGPE EFF+FDD+R+ A + G    ID  E  WNS   YE GN GHRPG+KGGY
Sbjct: 121 IADTAFFGPENEFFIFDDVRWSAEMGGCSYKIDSEEAGWNSEKVYENGNIGHRPGIKGGY 180

Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240
           FPVPPVDS QD+RS MCLV+E++G+  E HHHEVATAGQ E+  +FNT+ KKADE+   K
Sbjct: 181 FPVPPVDSFQDMRSAMCLVLEELGMTTEVHHHEVATAGQCEIGVKFNTLVKKADEVLELK 240

Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIG 300
           YVV N+AH +GKTATFMPKP+ GDNGSGMH H SLAK G NLFSGD Y GLSE ALYYIG
Sbjct: 241 YVVANIAHAYGKTATFMPKPLVGDNGSGMHVHQSLAKGGVNLFSGDLYGGLSETALYYIG 300

Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVR 360
           G+IKHAKA+NAL N +TNSYKRLVPG+EAPVMLAYSARNRSASIRIP V +PK RRIEVR
Sbjct: 301 GIIKHAKALNALTNASTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVTNPKGRRIEVR 360

Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420
           FPD  ANPYL F+A+LMAGLDGI+NKIHPGEAMDK+LYDLPPEE K IPQVA SL+ AL+
Sbjct: 361 FPDSTANPYLAFSAMLMAGLDGIQNKIHPGEAMDKDLYDLPPEEEKAIPQVAFSLDSALD 420

Query: 421 ALDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469
           ALD DREFL  GGVFTD+AID YI L+R++  R+RM+ HPVEF++YYS+
Sbjct: 421 ALDADREFLTRGGVFTDDAIDGYIELKRQDVTRLRMSTHPVEFDMYYSL 469


Lambda     K      H
   0.318    0.136    0.401 

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: 774
Number of extensions: 23
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_013819544.1 METME_RS14745 (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.3651.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.4e-209  679.9   0.0   9.5e-209  679.7   0.0    1.0  1  lcl|NCBI__GCF_000214665.1:WP_013819544.1  METME_RS14745 glutamate--ammonia


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214665.1:WP_013819544.1  METME_RS14745 glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  679.7   0.0  9.5e-209  9.5e-209       1     462 []       4     468 ..       4     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 679.7 bits;  conditional E-value: 9.5e-209
                                 TIGR00653   1 eevlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdp 69 
                                               e+vlk+++e++v+fvd+rf+D++Gk+++v++p+++++e+++eeg +FDgssv G+k+i+esD++l+pdp
  lcl|NCBI__GCF_000214665.1:WP_013819544.1   4 ENVLKMIQENDVQFVDFRFCDTRGKEQHVTFPAHTIDEDTFEEGNMFDGSSVAGWKHINESDMILMPDP 72 
                                               6799***************************************************************** PP

                                 TIGR00653  70 etlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvef 137
                                               +t++i+Pf ++k+++++cd+ ep +++ y rdpRsiakrae +++ t+++d+++fGpE+EFf+fd+v+ 
  lcl|NCBI__GCF_000214665.1:WP_013819544.1  73 STAKIDPFFDDKTVILRCDIIEPKDMQGYGRDPRSIAKRAEAYMQsTGIADTAFFGPENEFFIFDDVRW 141
                                               ********************************************************************* PP

                                 TIGR00653 138 keasnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevs 204
                                               + ++    +++dsee+ wn  + +e+gn g+++  kggYf+v+pvD+ +d+r+ ++l+leelg+++ev+
  lcl|NCBI__GCF_000214665.1:WP_013819544.1 142 SAEMGGCSYKIDSEEAGWNseKVYENGNIGHRPGIKGGYFPVPPVDSFQDMRSAMCLVLEELGMTTEVH 210
                                               *******************98899********************************************* PP

                                 TIGR00653 205 HHEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdg 272
                                               HHEvata q Ei++kf++lvk+aDe++ +Kyvv n+a+ +GktatFmpKpl+gdngsGmHvh+sl k g
  lcl|NCBI__GCF_000214665.1:WP_013819544.1 211 HHEVATAgQCEIGVKFNTLVKKADEVLELKYVVANIAHAYGKTATFMPKPLVGDNGSGMHVHQSLAKGG 279
                                               ********************************************************************* PP

                                 TIGR00653 273 enlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiP 341
                                                nlf+g+  y gLsetalyyigGi+kHakal+Altn+++nsYkRLvpG+EAPv+laysa+nRsa+iRiP
  lcl|NCBI__GCF_000214665.1:WP_013819544.1 280 VNLFSGDL-YGGLSETALYYIGGIIKHAKALNALTNASTNSYKRLVPGFEAPVMLAYSARNRSASIRIP 347
                                               ********.************************************************************ PP

                                 TIGR00653 342 asanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpes 410
                                               +++npk++RiEvR+pD++anpYLaf+a+lmAgldGi+nki+pge++dk+ly+l++ee k   i+q++ s
  lcl|NCBI__GCF_000214665.1:WP_013819544.1 348 YVTNPKGRRIEVRFPDSTANPYLAFSAMLMAGLDGIQNKIHPGEAMDKDLYDLPPEEEKA--IPQVAFS 414
                                               *********************************************************999..******* PP

                                 TIGR00653 411 Leealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                               L+ ald+l++d+  ++ ++v+++++i+ +ielkr++v +lr++ hpvE+ +y++
  lcl|NCBI__GCF_000214665.1:WP_013819544.1 415 LDSALDALDADRefLTRGGVFTDDAIDGYIELKRQDVTRLRMSTHPVEFDMYYS 468
                                               ************888999**********************************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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.86
//
[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