Alignments for a candidate for glnA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Dinoroseobacter shibae DFL-12

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate 3608443 Dshi_1839 glutamine synthetase, type I (RefSeq)

Query= BRENDA::P0A1P6
         (469 letters)



>FitnessBrowser__Dino:3608443
          Length = 468

 Score =  617 bits (1590), Expect = 0.0
 Identities = 291/468 (62%), Positives = 367/468 (78%), Gaps = 1/468 (0%)

Query: 1   MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60
           MS + VL  + + E+++VD+RFTD +GK QHVT+ A QV+A+F EEG MFDGSSI GWK 
Sbjct: 1   MSKDAVLKTIADEEIEYVDIRFTDPRGKLQHVTVIADQVDADFLEEGFMFDGSSIAGWKS 60

Query: 61  INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATG 120
           I++SDM LMPD ++A +DPF+A+ TL + C I+EP T + YDRDPR  A++AE YL+++G
Sbjct: 61  IDQSDMKLMPDTNSAYVDPFYAEKTLCLHCSIVEPDTGEAYDRDPRGTAEKAEAYLKSSG 120

Query: 121 IADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGY 180
           I D   FGPE EFFLFDD+RF   ++     +D  + AWNS  +YE GN GHRPG+KGGY
Sbjct: 121 IGDVAYFGPEAEFFLFDDVRFSVEMNKVSFEVDAQDAAWNSDAEYEMGNMGHRPGIKGGY 180

Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240
           FPV P+D+AQD+RSEM   M++MG+ V+ HHHEVA+  Q+E+   F ++T +ADE+Q YK
Sbjct: 181 FPVNPIDAAQDLRSEMLSTMKRMGMKVDKHHHEVASC-QHELGLIFGSLTHQADELQKYK 239

Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIG 300
           YV+HNVAH +GK+ATFMPKP+ GDNG+GMH +MS+ K+G  LF+GDKYA LS++ALY+IG
Sbjct: 240 YVIHNVAHAYGKSATFMPKPIAGDNGTGMHVNMSIWKDGKPLFAGDKYADLSQEALYFIG 299

Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVR 360
           G++KHAKA+NA  NP+TNSYKRL+PG+EAPV+ AYSARNRS  +RIP   SPKA+R+E R
Sbjct: 300 GILKHAKALNAFTNPSTNSYKRLIPGFEAPVLRAYSARNRSGCVRIPWAESPKAKRVEAR 359

Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420
           FPDPAANPYLCFAALLMAGLDGIKNKI PGEA DK+LYDLPPEE  EIP V  SL EAL+
Sbjct: 360 FPDPAANPYLCFAALLMAGLDGIKNKIDPGEASDKDLYDLPPEELAEIPTVCASLREALD 419

Query: 421 ALDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYS 468
           AL+ D EFL AG VFT + ID Y  L+ EE      TPHPVE++LYYS
Sbjct: 420 ALEADHEFLLAGDVFTKDQIDGYCELKWEEVYAYEHTPHPVEYKLYYS 467


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: 726
Number of extensions: 27
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: 469
Length of database: 468
Length adjustment: 33
Effective length of query: 436
Effective length of database: 435
Effective search space:   189660
Effective search space used:   189660
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 3608443 Dshi_1839 (glutamine synthetase, type I (RefSeq))
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.8960.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.6e-200  651.9   0.0     3e-200  651.7   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608443  Dshi_1839 glutamine synthetase, 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608443  Dshi_1839 glutamine synthetase, type I (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  651.7   0.0    3e-200    3e-200       2     462 .]       5     467 ..       4     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 651.7 bits;  conditional E-value: 3e-200
                         TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvivPfr 78 
                                        vlk++ +e++++vd+rf+D +Gkl++v++ ++++++++leeg +FDgss+ G+ksi++sD+ l+pd++++ ++Pf 
  lcl|FitnessBrowser__Dino:3608443   5 AVLKTIADEEIEYVDIRFTDPRGKLQHVTVIADQVDADFLEEGFMFDGSSIAGWKSIDQSDMKLMPDTNSAYVDPFY 81 
                                       578999*********************************************************************** PP

                         TIGR00653  79 aekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflevdseege 154
                                       aek+l + c++ ep t+e y+rdpR +a++ae +lk +++gd +yfGpEaEFflfd+v+f+ ++n+  +evd+++++
  lcl|FitnessBrowser__Dino:3608443  82 AEKTLCLHCSIVEPDTGEAYDRDPRGTAEKAEAYLKsSGIGDVAYFGPEAEFFLFDDVRFSVEMNKVSFEVDAQDAA 158
                                       ************************************99*************************************** PP

                         TIGR00653 155 wn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvataqaEidikfdklvkaaDei 229
                                       wn  +e+e gn g+++  kggYf+v+p+D a+d+r+e++++++++g++v+++HHEva+ q+E+++ f +l+++aDe+
  lcl|FitnessBrowser__Dino:3608443 159 WNsdAEYEMGNMGHRPGIKGGYFPVNPIDAAQDLRSEMLSTMKRMGMKVDKHHHEVASCQHELGLIFGSLTHQADEL 235
                                       **9999999******************************************************************** PP

                         TIGR00653 230 vlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHakalaAl 306
                                       ++yKyv++nva+ +Gk atFmpKp+ gdng GmHv++s+wkdg++lfag++ ya+Ls++aly+igGilkHakal+A+
  lcl|FitnessBrowser__Dino:3608443 236 QKYKYVIHNVAHAYGKSATFMPKPIAGDNGTGMHVNMSIWKDGKPLFAGDK-YADLSQEALYFIGGILKHAKALNAF 311
                                       ***************************************************.************************* PP

                         TIGR00653 307 tnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkidp 383
                                       tnp++nsYkRL+pG+EAPv  aysa+nRs ++RiP + +pkakR+E R+pDp+anpYL+faallmAgldGiknkidp
  lcl|FitnessBrowser__Dino:3608443 312 TNPSTNSYKRLIPGFEAPVLRAYSARNRSGCVRIPWAESPKAKRVEARFPDPAANPYLCFAALLMAGLDGIKNKIDP 388
                                       ***************************************************************************** PP

                         TIGR00653 384 gepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvEle 458
                                       ge+ dk+ly+l++eel+e  i+++ +sL+eald+le+d+  +++++v++++ i+ + elk +Ev  ++ ++hpvE +
  lcl|FitnessBrowser__Dino:3608443 389 GEASDKDLYDLPPEELAE--IPTVCASLREALDALEADHefLLAGDVFTKDQIDGYCELKWEEVYAYEHTPHPVEYK 463
                                       ******************..*******************98899********************************* PP

                         TIGR00653 459 kyld 462
                                        y++
  lcl|FitnessBrowser__Dino:3608443 464 LYYS 467
                                       **95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (468 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 9.27
//
[ok]

This GapMind analysis is from Apr 09 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