Alignments for a candidate for glnA in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Pseudomonas fluorescens FW300-N2E3

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate AO353_12170 AO353_12170 glutamine synthetase

Query= SwissProt::Q3V5W6
         (468 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_12170
          Length = 468

 Score =  915 bits (2364), Expect = 0.0
 Identities = 442/468 (94%), Positives = 456/468 (97%)

Query: 1   MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGI 60
           MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDAL++ FFE GKMFDGSSIAGWKGI
Sbjct: 1   MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALDEAFFEEGKMFDGSSIAGWKGI 60

Query: 61  EASDMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGI 120
           EASDMIL+PDD TAVLDPFTE+ TLILVCD+IEPSTMQGYDRDPRAIA RAEEYLK+TGI
Sbjct: 61  EASDMILMPDDTTAVLDPFTEEPTLILVCDVIEPSTMQGYDRDPRAIAKRAEEYLKSTGI 120

Query: 121 GDTVFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYF 180
           GDTVF GPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQD+EGGNKGHRPGVKGGYF
Sbjct: 121 GDTVFVGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDVEGGNKGHRPGVKGGYF 180

Query: 181 PVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKY 240
           PVPPFDHDHEIRT+MCNA+EEMG  +EVHHHEVATAGQNEIGVKFNTLV KADEVQTLKY
Sbjct: 181 PVPPFDHDHEIRTSMCNAMEEMGLVIEVHHHEVATAGQNEIGVKFNTLVAKADEVQTLKY 240

Query: 241 VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGG 300
            VHNVADAYGRTATFMPKPLYGDNGSGMHVH+SIAKDGKNTFAGEGYAGLS+TALYFIGG
Sbjct: 241 CVHNVADAYGRTATFMPKPLYGDNGSGMHVHLSIAKDGKNTFAGEGYAGLSDTALYFIGG 300

Query: 301 IIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARF 360
           IIKHGKALNGFTNP+TNSYKRLVPGFEAPVMLAYSARNRSASIRIPYV+SPR RRIEARF
Sbjct: 301 IIKHGKALNGFTNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVSSPRARRIEARF 360

Query: 361 PDPAANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE 420
           PDPAANPYL FAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE
Sbjct: 361 PDPAANPYLGFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE 420

Query: 421 LDKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYSC 468
           LDKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYSC
Sbjct: 421 LDKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYSC 468


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: 944
Number of extensions: 39
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: 468
Length of database: 468
Length adjustment: 33
Effective length of query: 435
Effective length of database: 435
Effective search space:   189225
Effective search space used:   189225
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 AO353_12170 AO353_12170 (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.10683.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   3.1e-204  664.8   0.0   3.5e-204  664.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12170  AO353_12170 glutamine synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_12170  AO353_12170 glutamine synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  664.7   0.0  3.5e-204  3.5e-204       4     462 .]       5     467 ..       2     467 .. 0.98

  Alignments for each domain:
  == domain 1  score: 664.7 bits;  conditional E-value: 3.5e-204
                                     TIGR00653   4 lkllkeenvkfvdlrfvDikGklkkveipvse.leeealeegiaFDgssveGfksieesDlllkp 67 
                                                   ++l+k+++vk +dlrf+D+kG+ ++v++p+++ l+e ++eeg++FDgss+ G+k+ie sD++l+p
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12170   5 VQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDaLDEAFFEEGKMFDGSSIAGWKGIEASDMILMP 69 
                                                   6899*************************985267999*************************** PP

                                     TIGR00653  68 dpetlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFfl 131
                                                   d  t+v +Pf++e++l+++cdv ep t++ y+rdpR iakraee+lk t++gd+v++GpE+EFf+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12170  70 DDTTAVLDPFTEEPTLILVCDVIEPSTMQGYDRDPRAIAKRAEEYLKsTGIGDTVFVGPEPEFFI 134
                                                   ***************************************************************** PP

                                     TIGR00653 132 fdkvefkeasnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlal 194
                                                   fd+v+fk+  + s++++ se+g+w   ++ve+gnkg+++  kggYf+v+p D+ ++ir+++++a+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12170 135 FDEVKFKSDISGSMFKIYSEQGSWMsdQDVEGGNKGHRPGVKGGYFPVPPFDHDHEIRTSMCNAM 199
                                                   ************************988899999******************************** PP

                                     TIGR00653 195 eelglevevsHHEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdn 258
                                                   ee+gl +ev+HHEvata q+Ei++kf++lv +aDe++++Ky v+nva+ +G+tatFmpKpl+gdn
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12170 200 EEMGLVIEVHHHEVATAgQNEIGVKFNTLVAKADEVQTLKYCVHNVADAYGRTATFMPKPLYGDN 264
                                                   ***************************************************************** PP

                                     TIGR00653 259 gsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEA 323
                                                   gsGmHvhls+ kdg+n fage  yagLs+taly+igGi+kH+kal+ +tnp++nsYkRLvpG+EA
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12170 265 GSGMHVHLSIAKDGKNTFAGEG-YAGLSDTALYFIGGIIKHGKALNGFTNPSTNSYKRLVPGFEA 328
                                                   *********************9.****************************************** PP

                                     TIGR00653 324 PvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepld 388
                                                   Pv+laysa+nRsa+iRiP++++p+a+RiE R+pDp+anpYL faallmAgldGi+nki+pg++ d
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12170 329 PVMLAYSARNRSASIRIPYVSSPRARRIEARFPDPAANPYLGFAALLMAGLDGIQNKIHPGDAAD 393
                                                   ***************************************************************** PP

                                     TIGR00653 389 knlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlk 451
                                                   knly+l++ee+ke  i+q+  sL+eal+el++ +  +++++v+++++i+a+i+lk +E  ++r+ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12170 394 KNLYDLPPEEAKE--IPQVCGSLKEALEELDKGRafLTKGGVFSDDFIDAYIALKSEEEIKVRTF 456
                                                   *************..******************99999*************************** PP

                                     TIGR00653 452 vhpvElekyld 462
                                                   vhp+E e y++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12170 457 VHPLEYELYYS 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.54
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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