Alignments for a candidate for glnA in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Paraburkholderia bryophila 376MFSha3.1

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate H281DRAFT_00452 H281DRAFT_00452 L-glutamine synthetase

Query= SwissProt::Q3V5W6
         (468 letters)



>FitnessBrowser__Burk376:H281DRAFT_00452
          Length = 471

 Score =  653 bits (1684), Expect = 0.0
 Identities = 311/471 (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
           ++G+GDT F GPEPEFFIFD V++ +D SG   KI SE+  W S ++ EGGN GHRPG K
Sbjct: 120 SSGLGDTAFFGPEPEFFIFDSVQWNTDQSGCFVKIGSEEAPWSSSKEFEGGNTGHRPGTK 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++ NVA  YG+TATFMPKP+ GDNGSGMHVH SI KDG+N FAG GYAGLSE AL+
Sbjct: 240 QMKYIIQNVAHTYGKTATFMPKPIVGDNGSGMHVHQSIWKDGQNLFAGNGYAGLSEFALF 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 ALDALDGDREFLTRGGVFTDSMLDAYIELKTNELQRYRQSVHPIEFEMYYS 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: 766
Number of extensions: 22
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 H281DRAFT_00452 H281DRAFT_00452 (L-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.23241.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.2e-205  667.7   0.0   4.7e-205  667.5   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00452  H281DRAFT_00452 L-glutamine synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00452  H281DRAFT_00452 L-glutamine synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  667.5   0.0  4.7e-205  4.7e-205       2     462 .]       7     470 ..       6     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: 667.5 bits;  conditional E-value: 4.7e-205
                                    TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkp 67 
                                                  +v++l+k+e+vkfvd+rf+D++Gk+++v++pvs+++e+ +e+g aFDgss+ G+k+ie sD+ll+p
  lcl|FitnessBrowser__Burk376:H281DRAFT_00452   7 DVVQLVKDEDVKFVDFRFTDTRGKEQHVSVPVSAFDEDKFESGHAFDGSSIAGWKGIEASDMLLVP 72 
                                                  68899************************************************************* PP

                                    TIGR00653  68 dpetlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflf 132
                                                  d++t++i+Pf +e++l+++cdv ep++++ yerdpRs akrae +lk ++lgd+++fGpE+EFf+f
  lcl|FitnessBrowser__Burk376:H281DRAFT_00452  73 DANTAFIDPFYEESTLVLTCDVVEPADGKGYERDPRSLAKRAEAYLKsSGLGDTAFFGPEPEFFIF 138
                                                  ***********************************************99***************** PP

                                    TIGR00653 133 dkvefkeasnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlalee 196
                                                  d+v+ ++ ++  f+++ see+ w+  +e+e+gn+g+++ +kggYf+v+pvD+ +dir+e++l le+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00452 139 DSVQWNTDQSGCFVKIGSEEAPWSssKEFEGGNTGHRPGTKGGYFPVAPVDTFQDIRSEMCLLLEQ 204
                                                  ***********************999999************************************* PP

                                    TIGR00653 197 lglevevsHHEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsG 261
                                                  +g+ vev+HHEva   q+Ei++kf++lv+ aD ++++Ky+++nva+ +GktatFmpKp++gdngsG
  lcl|FitnessBrowser__Burk376:H281DRAFT_00452 205 IGIPVEVHHHEVAGQgQNEIGTKFSTLVQRADWLQQMKYIIQNVAHTYGKTATFMPKPIVGDNGSG 270
                                                  ************9666************************************************** PP

                                    TIGR00653 262 mHvhlslwkdgenlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvyl 327
                                                  mHvh+s+wkdg+nlfag+  yagLse al+yigGi+kHa+al+A+tnp++nsYkRLvp +EAPv+l
  lcl|FitnessBrowser__Burk376:H281DRAFT_00452 271 MHVHQSIWKDGQNLFAGNG-YAGLSEFALFYIGGIIKHARALNAITNPSTNSYKRLVPHFEAPVKL 335
                                                  ******************9.********************************************** PP

                                    TIGR00653 328 aysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlye 393
                                                  aysa+nRsa+iRiP ++npk++RiE R+pDp anpYL+f+al+mAgldG++nki+pge+ dknly+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00452 336 AYSARNRSASIRIPHVSNPKGRRIETRFPDPMANPYLCFSALMMAGLDGVQNKIHPGEAADKNLYD 401
                                                  ****************************************************************** PP

                                    TIGR00653 394 lseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvEl 457
                                                  l++ee ++  i+++ + L++ald+l+ d+  ++ ++v+++ +++a+ielk++E +++r +vhp+E+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00452 402 LPPEEDAK--IPTVCAGLDQALDALDGDRefLTRGGVFTDSMLDAYIELKTNELQRYRQSVHPIEF 465
                                                  ********..*******************888999******************************* PP

                                    TIGR00653 458 ekyld 462
                                                  e+y++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00452 466 EMYYS 470
                                                  ***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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.62
//
[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