Alignments for a candidate for glnA in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Burkholderia phytofirmans PsJN

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate BPHYT_RS12945 BPHYT_RS12945 glutamine synthetase

Query= SwissProt::Q3V5W6
         (468 letters)



>FitnessBrowser__BFirm:BPHYT_RS12945
          Length = 471

 Score =  655 bits (1691), Expect = 0.0
 Identities = 313/471 (66%), Positives = 380/471 (80%), Gaps = 5/471 (1%)

Query: 1   MSKSV----QLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAG 56
           MSKSV    QL+KD DVK++D RFTDT+G + HV++P   A ++D FE G  FDGSSIAG
Sbjct: 1   MSKSVADVVQLVKDEDVKFVDFRFTDTRGKEQHVSVPV-SAFDEDKFESGHAFDGSSIAG 59

Query: 57  WKGIEASDMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLK 116
           WKGIEASDM+L+PD +TA +DPF E++TL+L CD++EP+  +GY+RDPR++A RAE YLK
Sbjct: 60  WKGIEASDMLLVPDANTAFIDPFYEESTLVLTCDVVEPADGKGYERDPRSLAKRAEAYLK 119

Query: 117 TTGIGDTVFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVK 176
           +TG+GDT F GPEPEFFIFD V++ +D SG   KI SE+  W S ++ EGGN GHRPG K
Sbjct: 120 STGLGDTAFFGPEPEFFIFDSVQWNTDQSGCFIKIGSEEAPWSSAKEFEGGNTGHRPGTK 179

Query: 177 GGYFPVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQ 236
           GGYFPV P D   +IR+ MC  LE++G  VEVHHHEVA  GQNEIG KF+TLV++AD +Q
Sbjct: 180 GGYFPVAPVDTFQDIRSEMCLLLEQIGIPVEVHHHEVAGQGQNEIGTKFSTLVQRADWLQ 239

Query: 237 TLKYVVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALY 296
            +KY++HNVA  YG+TATFMPKP+ GDNGSGMHVH SI KDG N FAG GYAGLSE AL+
Sbjct: 240 QMKYIIHNVAHTYGKTATFMPKPVVGDNGSGMHVHQSIWKDGANLFAGNGYAGLSEFALF 299

Query: 297 FIGGIIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRI 356
           +IGGIIKH +ALN  TNP+TNSYKRLVP FEAPV LAYSARNRSASIRIP+V++P+GRRI
Sbjct: 300 YIGGIIKHARALNAITNPSTNSYKRLVPHFEAPVKLAYSARNRSASIRIPHVSNPKGRRI 359

Query: 357 EARFPDPAANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKE 416
           E RFPDP ANPYL F+AL+MAGLDG+QNKIHPG+AADKNLYDLPPEE  +IP VC  L +
Sbjct: 360 ETRFPDPMANPYLCFSALMMAGLDGVQNKIHPGEAADKNLYDLPPEEDAKIPTVCAGLDQ 419

Query: 417 ALEELDKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYS 467
           AL+ LD  R FLT+GGVF+D  +DAYI LK+ E  + R  VHP+E+E+YYS
Sbjct: 420 ALDALDADREFLTRGGVFTDSMLDAYIELKTGELQRYRQSVHPIEFEMYYS 470


Lambda     K      H
   0.318    0.137    0.409 

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: 769
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: 468
Length of database: 471
Length adjustment: 33
Effective length of query: 435
Effective length of database: 438
Effective search space:   190530
Effective search space used:   190530
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 BPHYT_RS12945 BPHYT_RS12945 (glutamine synthetase)
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.5217.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-204  665.1   0.0     3e-204  664.9   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS12945  BPHYT_RS12945 glutamine syntheta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS12945  BPHYT_RS12945 glutamine synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  664.9   0.0    3e-204    3e-204       2     462 .]       7     470 ..       6     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: 664.9 bits;  conditional E-value: 3e-204
                                TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpet 71 
                                              +v++l+k+e+vkfvd+rf+D++Gk+++v++pvs+++e+ +e+g aFDgss+ G+k+ie sD+ll+pd++t
  lcl|FitnessBrowser__BFirm:BPHYT_RS12945   7 DVVQLVKDEDVKFVDFRFTDTRGKEQHVSVPVSAFDEDKFESGHAFDGSSIAGWKGIEASDMLLVPDANT 76 
                                              68899***************************************************************** PP

                                TIGR00653  72 lvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkea 140
                                              ++i+Pf +e++l+++cdv ep++++ yerdpRs akrae +lk t+lgd+++fGpE+EFf+fd+v+ ++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS12945  77 AFIDPFYEESTLVLTCDVVEPADGKGYERDPRSLAKRAEAYLKsTGLGDTAFFGPEPEFFIFDSVQWNTD 146
                                              ********************************************************************** PP

                                TIGR00653 141 snssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEv 208
                                              ++  f+++ see+ w+  +e+e+gn+g+++ +kggYf+v+pvD+ +dir+e++l le++g+ vev+HHEv
  lcl|FitnessBrowser__BFirm:BPHYT_RS12945 147 QSGCFIKIGSEEAPWSsaKEFEGGNTGHRPGTKGGYFPVAPVDTFQDIRSEMCLLLEQIGIPVEVHHHEV 216
                                              ***************999999************************************************* PP

                                TIGR00653 209 ata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfa 277
                                              a   q+Ei++kf++lv+ aD ++++Ky+++nva+ +GktatFmpKp++gdngsGmHvh+s+wkdg+nlfa
  lcl|FitnessBrowser__BFirm:BPHYT_RS12945 217 AGQgQNEIGTKFSTLVQRADWLQQMKYIIHNVAHTYGKTATFMPKPVVGDNGSGMHVHQSIWKDGANLFA 286
                                              9666****************************************************************** PP

                                TIGR00653 278 geegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpk 347
                                              g+  yagLse al+yigGi+kHa+al+A+tnp++nsYkRLvp +EAPv+laysa+nRsa+iRiP ++npk
  lcl|FitnessBrowser__BFirm:BPHYT_RS12945 287 GNG-YAGLSEFALFYIGGIIKHARALNAITNPSTNSYKRLVPHFEAPVKLAYSARNRSASIRIPHVSNPK 355
                                              **9.****************************************************************** PP

                                TIGR00653 348 akRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealde 417
                                              ++RiE R+pDp anpYL+f+al+mAgldG++nki+pge+ dknly+l++ee ++  i+++ + L++ald+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12945 356 GRRIETRFPDPMANPYLCFSALMMAGLDGVQNKIHPGEAADKNLYDLPPEEDAK--IPTVCAGLDQALDA 423
                                              ******************************************************..************** PP

                                TIGR00653 418 lesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                              l++d+  ++ ++v+++ +++a+ielk+ E +++r +vhp+E+e+y++
  lcl|FitnessBrowser__BFirm:BPHYT_RS12945 424 LDADRefLTRGGVFTDSMLDAYIELKTGELQRYRQSVHPIEFEMYYS 470
                                              *****888999**********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (471 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: 10.13
//
[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