GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glnA in Pseudomonas putida KT2440

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate PP_5046 PP_5046 glutamine synthetase

Query= SwissProt::Q3V5W6
         (468 letters)



>FitnessBrowser__Putida:PP_5046
          Length = 468

 Score =  901 bits (2328), Expect = 0.0
 Identities = 434/468 (92%), Positives = 454/468 (97%)

Query: 1   MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGI 60
           MSKSVQLIKDHDVKWIDLRFTDTKG QHHVTMP+RDAL++DFFEVGKMFDGSSIAGWKGI
Sbjct: 1   MSKSVQLIKDHDVKWIDLRFTDTKGIQHHVTMPSRDALDEDFFEVGKMFDGSSIAGWKGI 60

Query: 61  EASDMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGI 120
           EASDMIL+P D+TAVLDPFTE+ TLI+ CDI++PS+MQGYDRDPRAIA RAEEYLK+TGI
Sbjct: 61  EASDMILMPVDETAVLDPFTEEPTLIITCDIVDPSSMQGYDRDPRAIAKRAEEYLKSTGI 120

Query: 121 GDTVFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYF 180
           GDTVFAGPEPEFFIFDEVKF SDISGSMFKI+SEQGSWM+  D+EGGNKGHRPGVKGGYF
Sbjct: 121 GDTVFAGPEPEFFIFDEVKFHSDISGSMFKIFSEQGSWMTGADVEGGNKGHRPGVKGGYF 180

Query: 181 PVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKY 240
           PVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQ LKY
Sbjct: 181 PVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQALKY 240

Query: 241 VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGG 300
           VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSI KDGKNTF+GEGYAGLS+TALYFIGG
Sbjct: 241 VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIWKDGKNTFSGEGYAGLSDTALYFIGG 300

Query: 301 IIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARF 360
           IIKHGKALNGFTNP+TNSYKRLVPGFEAPVMLAYSARNRSASIRIPYV SP+ RRIEARF
Sbjct: 301 IIKHGKALNGFTNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVGSPKARRIEARF 360

Query: 361 PDPAANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE 420
           PDP+ANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAK IPQVCGSLKEALEE
Sbjct: 361 PDPSANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKNIPQVCGSLKEALEE 420

Query: 421 LDKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYSC 468
           LDKGRAFLTKGGVFSDDFIDA+I LKSEEEIKVRTFVHPLEYELYYSC
Sbjct: 421 LDKGRAFLTKGGVFSDDFIDAFIELKSEEEIKVRTFVHPLEYELYYSC 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: 947
Number of extensions: 33
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 PP_5046 PP_5046 (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.15679.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.4e-205  667.6   0.0   4.9e-205  667.5   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_5046  PP_5046 glutamine synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5046  PP_5046 glutamine synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  667.5   0.0  4.9e-205  4.9e-205       4     462 .]       5     467 ..       2     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 667.5 bits;  conditional E-value: 4.9e-205
                           TIGR00653   4 lkllkeenvkfvdlrfvDikGklkkveipvs.eleeealeegiaFDgssveGfksieesDlllkpdpetlvivPf 77 
                                         ++l+k+++vk +dlrf+D+kG+ ++v++p + +l+e+++e g++FDgss+ G+k+ie sD++l+p+ et+v +Pf
  lcl|FitnessBrowser__Putida:PP_5046   5 VQLIKDHDVKWIDLRFTDTKGIQHHVTMPSRdALDEDFFEVGKMFDGSSIAGWKGIEASDMILMPVDETAVLDPF 79 
                                         6899*************************872578**************************************** PP

                           TIGR00653  78 raekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflevdse 151
                                         ++e++l+++cd+ +p  ++ y+rdpR iakraee+lk t++gd+v+ GpE+EFf+fd+v+f++  + s++++ se
  lcl|FitnessBrowser__Putida:PP_5046  80 TEEPTLIITCDIVDPSSMQGYDRDPRAIAKRAEEYLKsTGIGDTVFAGPEPEFFIFDEVKFHSDISGSMFKIFSE 154
                                         *************************************************************************** PP

                           TIGR00653 152 egewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEidikfdklv 223
                                         +g+w   ++ve+gnkg+++  kggYf+v+p D+ ++ir+ +++alee+g +vev+HHEvata q+Ei++kf++lv
  lcl|FitnessBrowser__Putida:PP_5046 155 QGSWMtgADVEGGNKGHRPGVKGGYFPVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAgQNEIGVKFNTLV 229
                                         ****988999***************************************************************** PP

                           TIGR00653 224 kaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilk 298
                                         k+aDe++ +Kyvv+nva+ +G+tatFmpKpl+gdngsGmHvh+s+wkdg+n f+ge  yagLs+taly+igGi+k
  lcl|FitnessBrowser__Putida:PP_5046 230 KKADEVQALKYVVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIWKDGKNTFSGEG-YAGLSDTALYFIGGIIK 303
                                         ********************************************************9.***************** PP

                           TIGR00653 299 HakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAg 373
                                         H+kal+ +tnp++nsYkRLvpG+EAPv+laysa+nRsa+iRiP++ +pka+RiE R+pDpsanpYLafaallmAg
  lcl|FitnessBrowser__Putida:PP_5046 304 HGKALNGFTNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVGSPKARRIEARFPDPSANPYLAFAALLMAG 378
                                         *************************************************************************** PP

                           TIGR00653 374 ldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEve 446
                                         ldGi+nki+pg++ dknly+l++ee+k+  i+q+  sL+eal+el++ +  +++++v+++++i+afielk +E  
  lcl|FitnessBrowser__Putida:PP_5046 379 LDGIQNKIHPGDAADKNLYDLPPEEAKN--IPQVCGSLKEALEELDKGRafLTKGGVFSDDFIDAFIELKSEEEI 451
                                         ****************************..******************99999********************** PP

                           TIGR00653 447 elrlkvhpvElekyld 462
                                         ++r+ vhp+E e y++
  lcl|FitnessBrowser__Putida:PP_5046 452 KVRTFVHPLEYELYYS 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: 9.78
//
[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:

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:

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:

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:

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