Alignments for a candidate for glnA in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Acidovorax sp. GW101-3H11

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate Ac3H11_4429 Glutamine synthetase type I (EC 6.3.1.2)

Query= SwissProt::Q3V5W6
         (468 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4429
          Length = 497

 Score =  626 bits (1615), Expect = 0.0
 Identities = 301/463 (65%), Positives = 364/463 (78%), Gaps = 1/463 (0%)

Query: 5   VQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGIEASD 64
           ++++K+++VK+ID RFTDT+G Q H T+P     ED F   G  FDGSSIAGWKGIEASD
Sbjct: 35  MKMVKENEVKFIDFRFTDTRGKQQHTTVPVSHFDEDKFIS-GHAFDGSSIAGWKGIEASD 93

Query: 65  MILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGIGDTV 124
           M L+PD  TA +DPF E+ TLIL CD+IEP+  + YDRDPR+IA RAE YLK +G+GDT 
Sbjct: 94  MQLIPDPSTANIDPFFEETTLILTCDVIEPTDGKAYDRDPRSIAKRAEAYLKASGLGDTA 153

Query: 125 FAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYFPVPP 184
           + GPEPEFFIFD V++ ++ + + ++I   +  W +   +EGGN+GHRP VKGGYFPVPP
Sbjct: 154 YFGPEPEFFIFDGVRWSTEPNHTFYEIEEYEAPWNTGAKLEGGNRGHRPTVKGGYFPVPP 213

Query: 185 FDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKYVVHN 244
            D   ++R  M   LE +G  VEV HHEVA AGQNEIG +F+TLV++AD     KYV+HN
Sbjct: 214 VDSTQDMRAEMSLILESLGIPVEVFHHEVAGAGQNEIGTRFSTLVERADWTILQKYVIHN 273

Query: 245 VADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGGIIKH 304
           VA+AYG+TATFMPKP +GDNGSGMHVH S+ KDGKN FAG+GYAGLS+ ALY+IGGIIKH
Sbjct: 274 VANAYGKTATFMPKPYHGDNGSGMHVHQSVWKDGKNLFAGDGYAGLSDFALYYIGGIIKH 333

Query: 305 GKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARFPDPA 364
            +ALN  TNP TNSYKRLVP FEAPV LAYSA+NRSASIRIPYV +P+GRR+EARFPDP 
Sbjct: 334 ARALNAITNPGTNSYKRLVPHFEAPVKLAYSAKNRSASIRIPYVANPKGRRVEARFPDPL 393

Query: 365 ANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEELDKG 424
            NPYL FAALLMAGLDG++NKIHPG+AA K+LY LPPEE K +P VC SL +ALE LDK 
Sbjct: 394 MNPYLGFAALLMAGLDGVENKIHPGEAATKDLYHLPPEEDKLVPTVCHSLDQALEHLDKD 453

Query: 425 RAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYS 467
           RAFLTKGGVF+D  IDAYI LK  E  + R  VHP+EY++YYS
Sbjct: 454 RAFLTKGGVFTDSMIDAYIDLKMNEVTRFRMAVHPVEYDMYYS 496


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: 777
Number of extensions: 32
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: 497
Length adjustment: 34
Effective length of query: 434
Effective length of database: 463
Effective search space:   200942
Effective search space used:   200942
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: 52 (24.6 bits)

Align candidate Ac3H11_4429 (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.20953.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.9e-199  649.1   0.0   2.2e-199  648.9   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4429  Glutamine synthetase type I (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4429  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 !  648.9   0.0  2.2e-199  2.2e-199       2     462 .]      33     496 ..      32     496 .. 0.99

  Alignments for each domain:
  == domain 1  score: 648.9 bits;  conditional E-value: 2.2e-199
                                        TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDl 63 
                                                      +v+k++ke++vkf+d+rf+D++Gk ++ ++pvs+++e+ + +g aFDgss+ G+k+ie sD+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4429  33 DVMKMVKENEVKFIDFRFTDTRGKQQHTTVPVSHFDEDKFISGHAFDGSSIAGWKGIEASDM 94 
                                                      6899********************************************************** PP

                                        TIGR00653  64 llkpdpetlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfG 124
                                                       l pdp+t+ i+Pf +e++l+++cdv ep++++ y+rdpRsiakrae +lk ++lgd++yfG
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4429  95 QLIPDPSTANIDPFFEETTLILTCDVIEPTDGKAYDRDPRSIAKRAEAYLKaSGLGDTAYFG 156
                                                      ***************************************************9********** PP

                                        TIGR00653 125 pEaEFflfdkvefkeasnssflevdseegewn..reveegnkgykikkkggYfdvepvDkak 184
                                                      pE+EFf+fd v+ +++ n++f+e+++ e+ wn  ++ e+gn+g++++ kggYf+v+pvD+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4429 157 PEPEFFIFDGVRWSTEPNHTFYEIEEYEAPWNtgAKLEGGNRGHRPTVKGGYFPVPPVDSTQ 218
                                                      ********************************99999************************* PP

                                        TIGR00653 185 dirrelvlaleelglevevsHHEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGk 245
                                                      d+r e+ l+le+lg+ vev HHEva a q+Ei+++f++lv+ aD ++l Kyv++nva+ +Gk
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4429 219 DMRAEMSLILESLGIPVEVFHHEVAGAgQNEIGTRFSTLVERADWTILQKYVIHNVANAYGK 280
                                                      *************************999********************************** PP

                                        TIGR00653 246 tatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHakalaAlt 307
                                                      tatFmpKp  gdngsGmHvh+s+wkdg+nlfag+  yagLs+ alyyigGi+kHa+al+A+t
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4429 281 TATFMPKPYHGDNGSGMHVHQSVWKDGKNLFAGDG-YAGLSDFALYYIGGIIKHARALNAIT 341
                                                      **********************************9.************************** PP

                                        TIGR00653 308 nptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaal 369
                                                      np +nsYkRLvp +EAPv+laysaknRsa+iRiP++anpk++R+E R+pDp  npYL faal
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4429 342 NPGTNSYKRLVPHFEAPVKLAYSAKNRSASIRIPYVANPKGRRVEARFPDPLMNPYLGFAAL 403
                                                      ************************************************************** PP

                                        TIGR00653 370 lmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevl 429
                                                      lmAgldG++nki+pge+  k+ly+l++ee k   ++++ +sL++al++l++d+  +++++v+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4429 404 LMAGLDGVENKIHPGEAATKDLYHLPPEEDKL--VPTVCHSLDQALEHLDKDRafLTKGGVF 463
                                                      *****************************999..*******************9999***** PP

                                        TIGR00653 430 geelieafielkrkEveelrlkvhpvElekyld 462
                                                      ++ +i+a+i+lk++Ev ++r++vhpvE  +y++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4429 464 TDSMIDAYIDLKMNEVTRFRMAVHPVEYDMYYS 496
                                                      *******************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (497 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: 9.82
//
[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