Alignments for a candidate for glnA in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Pseudomonas stutzeri RCH2

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate GFF3858 Psest_3928 glutamine synthetase, type I

Query= SwissProt::Q3V5W6
         (468 letters)



>FitnessBrowser__psRCH2:GFF3858
          Length = 468

 Score =  882 bits (2279), Expect = 0.0
 Identities = 426/467 (91%), Positives = 448/467 (95%)

Query: 1   MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGI 60
           MSKS+QLIKD+DVKWIDLRFTDTKG QHHVT+PARDA ++DFFE GKMFDGSSI GWKGI
Sbjct: 1   MSKSLQLIKDYDVKWIDLRFTDTKGKQHHVTVPARDAQDEDFFEHGKMFDGSSIHGWKGI 60

Query: 61  EASDMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGI 120
           EASDMIL+P D+TAVLDPFTE+ TLILVCDI+EPSTMQGYDRDPR+IA RAEE+LKTTGI
Sbjct: 61  EASDMILMPVDETAVLDPFTEEPTLILVCDIVEPSTMQGYDRDPRSIAKRAEEFLKTTGI 120

Query: 121 GDTVFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYF 180
           GDTVF GPEPEFFIFD+VKFKSDISGSMFKIYSEQGSWM+DQD+EGGNKGHRP VKGGYF
Sbjct: 121 GDTVFVGPEPEFFIFDQVKFKSDISGSMFKIYSEQGSWMTDQDVEGGNKGHRPAVKGGYF 180

Query: 181 PVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKY 240
           PVPP DHDHEIRTAMCNA+E+MG  VEVHHHEVATAGQNEIGVKFNTLV KADEVQTLKY
Sbjct: 181 PVPPCDHDHEIRTAMCNAMEDMGLVVEVHHHEVATAGQNEIGVKFNTLVAKADEVQTLKY 240

Query: 241 VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGG 300
            VHNVADAYG+TATFMPKPLYGDNGSGMHVHMSI+KDGKNTFAGEGYAGLSETALYFIGG
Sbjct: 241 CVHNVADAYGKTATFMPKPLYGDNGSGMHVHMSISKDGKNTFAGEGYAGLSETALYFIGG 300

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

Query: 361 PDPAANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE 420
           PDPAANPYL FAALLMAGLDGIQNKIHPGDAADKNLYDLPPEE K IPQVCGSLKEALEE
Sbjct: 361 PDPAANPYLCFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEGKLIPQVCGSLKEALEE 420

Query: 421 LDKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYS 467
           LDKGRAFLTKGGVFSD+FIDAYI LKSEEEIKVRTFVHPLEY+LYYS
Sbjct: 421 LDKGRAFLTKGGVFSDEFIDAYIELKSEEEIKVRTFVHPLEYDLYYS 467


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: 908
Number of extensions: 34
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 GFF3858 Psest_3928 (glutamine synthetase, type I)
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.3071474.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.7e-204  665.0   0.0   3.1e-204  664.8   0.0    1.0  1  FitnessBrowser__psRCH2:GFF3858  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__psRCH2:GFF3858  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  664.8   0.0  3.1e-204  3.1e-204       4     462 .]       5     467 ..       2     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 664.8 bits;  conditional E-value: 3.1e-204
                       TIGR00653   4 lkllkeenvkfvdlrfvDikGklkkveipvsele.eealeegiaFDgssveGfksieesDlllkpdpetlvivPfraek 81 
                                     l+l+k+ +vk +dlrf+D+kGk ++v++p+++ + e+++e+g++FDgss++G+k+ie sD++l+p+ et+v +Pf++e+
  FitnessBrowser__psRCH2:GFF3858   5 LQLIKDYDVKWIDLRFTDTKGKQHHVTVPARDAQdEDFFEHGKMFDGSSIHGWKGIEASDMILMPVDETAVLDPFTEEP 83 
                                     6899**************************9887699****************************************** PP

                       TIGR00653  82 vlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflevdseegewn..r 157
                                     +l+++cd+ ep t++ y+rdpRsiakraee lk t++gd+v++GpE+EFf+fd+v+fk+  + s++++ se+g+w   +
  FitnessBrowser__psRCH2:GFF3858  84 TLILVCDIVEPSTMQGYDRDPRSIAKRAEEFLKtTGIGDTVFVGPEPEFFIFDQVKFKSDISGSMFKIYSEQGSWMtdQ 162
                                     *********************************9*****************************************9888 PP

                       TIGR00653 158 eveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEidikfdklvkaaDeivlyKyv 235
                                     +ve+gnkg++++ kggYf+v+p D+ ++ir+ +++a+e++gl vev+HHEvata q+Ei++kf++lv +aDe++++Ky 
  FitnessBrowser__psRCH2:GFF3858 163 DVEGGNKGHRPAVKGGYFPVPPCDHDHEIRTAMCNAMEDMGLVVEVHHHEVATAgQNEIGVKFNTLVAKADEVQTLKYC 241
                                     89999************************************************************************** PP

                       TIGR00653 236 vknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHakalaAltnptvnsY 314
                                     v+nva+ +GktatFmpKpl+gdngsGmHvh+s++kdg+n fage  yagLsetaly+igGi+kH+kal+ +tnp++nsY
  FitnessBrowser__psRCH2:GFF3858 242 VHNVADAYGKTATFMPKPLYGDNGSGMHVHMSISKDGKNTFAGEG-YAGLSETALYFIGGIIKHGKALNGFTNPATNSY 319
                                     ********************************************9.********************************* PP

                       TIGR00653 315 kRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlye 393
                                     kRLvpG+EAPv+laysa+nRsa+iRiP++++pka+RiE R+pDp+anpYL+faallmAgldGi+nki+pg++ dknly+
  FitnessBrowser__psRCH2:GFF3858 320 KRLVPGFEAPVMLAYSARNRSASIRIPYVSSPKARRIEARFPDPAANPYLCFAALLMAGLDGIQNKIHPGDAADKNLYD 398
                                     ******************************************************************************* PP

                       TIGR00653 394 lseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                     l++ee k   i+q+  sL+eal+el++ +  +++++v+++e+i+a+ielk +E  ++r+ vhp+E   y++
  FitnessBrowser__psRCH2:GFF3858 399 LPPEEGKL--IPQVCGSLKEALEELDKGRafLTKGGVFSDEFIDAYIELKSEEEIKVRTFVHPLEYDLYYS 467
                                     ******99..******************99999************************************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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.78
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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