Alignments for a candidate for glnA in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Pseudomonas fluorescens GW456-L13

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate PfGW456L13_342 Glutamine synthetase type I (EC 6.3.1.2)

Query= SwissProt::Q3V5W6
         (468 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_342
          Length = 468

 Score =  920 bits (2378), Expect = 0.0
 Identities = 447/468 (95%), Positives = 458/468 (97%)

Query: 1   MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGI 60
           MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDAL+DDFFEVGKMFDGSSIAGWKGI
Sbjct: 1   MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALDDDFFEVGKMFDGSSIAGWKGI 60

Query: 61  EASDMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGI 120
           EASDMIL+PDD TAVLDPFTE+ TLILVCDIIEPS+MQGYDRDPRAIA RAEE+LK T I
Sbjct: 61  EASDMILMPDDSTAVLDPFTEEPTLILVCDIIEPSSMQGYDRDPRAIAKRAEEHLKATAI 120

Query: 121 GDTVFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYF 180
           GDTV+AGPEPEFFIFD+VKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYF
Sbjct: 121 GDTVYAGPEPEFFIFDQVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYF 180

Query: 181 PVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKY 240
           PVPPFDHDHEIRT+MCNALEEMG TVEVHHHEVATAGQNEIGVKFNTLVKKADE QTLKY
Sbjct: 181 PVPPFDHDHEIRTSMCNALEEMGLTVEVHHHEVATAGQNEIGVKFNTLVKKADETQTLKY 240

Query: 241 VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGG 300
           VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSI KDGKNTFAGEGYAGLS+TALYFIGG
Sbjct: 241 VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIWKDGKNTFAGEGYAGLSDTALYFIGG 300

Query: 301 IIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARF 360
           IIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYV+SP+ RRIEARF
Sbjct: 301 IIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVSSPKARRIEARF 360

Query: 361 PDPAANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE 420
           PDPAANPYL FAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE
Sbjct: 361 PDPAANPYLCFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE 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: 950
Number of extensions: 36
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 PfGW456L13_342 (Glutamine synthetase type I (EC 6.3.1.2))
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.17494.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
   1.3e-206  672.7   0.0   1.5e-206  672.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_342  Glutamine synthetase type I (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_342  Glutamine synthetase type I (EC 6.3.1.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  672.5   0.0  1.5e-206  1.5e-206       4     462 .]       5     467 ..       2     467 .. 0.98

  Alignments for each domain:
  == domain 1  score: 672.5 bits;  conditional E-value: 1.5e-206
                                              TIGR00653   4 lkllkeenvkfvdlrfvDikGklkkveipvs.eleeealeegiaFDgssveGfksi 58 
                                                            ++l+k+++vk +dlrf+D+kG+ ++v++p++ +l+++++e g++FDgss+ G+k+i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_342   5 VQLIKDHDVKWIDLRFTDTKGTQHHVTMPARdALDDDFFEVGKMFDGSSIAGWKGI 60 
                                                            6899*************************9825789******************** PP

                                              TIGR00653  59 eesDlllkpdpetlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk 114
                                                            e sD++l+pd +t+v +Pf++e++l+++cd+ ep  ++ y+rdpR iakraee+lk
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_342  61 EASDMILMPDDSTAVLDPFTEEPTLILVCDIIEPSSMQGYDRDPRAIAKRAEEHLK 116
                                                            ******************************************************** PP

                                              TIGR00653 115 .tklgdevyfGpEaEFflfdkvefkeasnssflevdseegewn..reveegnkgyk 167
                                                             t +gd+vy GpE+EFf+fd+v+fk+  + s++++ se+g+w   +++e+gnkg++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_342 117 aTAIGDTVYAGPEPEFFIFDQVKFKSDISGSMFKIYSEQGSWMsdQDIEGGNKGHR 172
                                                            ******************************************988889999***** PP

                                              TIGR00653 168 ikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEidikfdkl 222
                                                            +  kggYf+v+p D+ ++ir+++++alee+gl+vev+HHEvata q+Ei++kf++l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_342 173 PGVKGGYFPVPPFDHDHEIRTSMCNALEEMGLTVEVHHHEVATAgQNEIGVKFNTL 228
                                                            ******************************************************** PP

                                              TIGR00653 223 vkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfag 278
                                                            vk+aDe++++Kyvv+nva+ +G+tatFmpKpl+gdngsGmHvh+s+wkdg+n fag
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_342 229 VKKADETQTLKYVVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIWKDGKNTFAG 284
                                                            ******************************************************** PP

                                              TIGR00653 279 eegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknR 334
                                                            e  yagLs+taly+igGi+kH+kal+ +tnp++nsYkRLvpG+EAPv+laysa+nR
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_342 285 EG-YAGLSDTALYFIGGIIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNR 339
                                                            *9.***************************************************** PP

                                              TIGR00653 335 saliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldkn 390
                                                            sa+iRiP++++pka+RiE R+pDp+anpYL+faallmAgldGi+nki+pg++ dkn
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_342 340 SASIRIPYVSSPKARRIEARFPDPAANPYLCFAALLMAGLDGIQNKIHPGDAADKN 395
                                                            ******************************************************** PP

                                              TIGR00653 391 lyelseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkE 444
                                                            ly+l++ee+ke  i+q+  sL+eal+el++ +  +++++v+++++i+a+i+lk +E
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_342 396 LYDLPPEEAKE--IPQVCGSLKEALEELDKGRafLTKGGVFSDDFIDAYIALKSEE 449
                                                            ***********..******************99999******************** PP

                                              TIGR00653 445 veelrlkvhpvElekyld 462
                                                              ++r+ vhp+E e y++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_342 450 EIKVRTFVHPLEYELYYS 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: 00:00:00.01
# Mc/sec: 12.20
//
[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