Alignments for a candidate for glnA in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Dechlorosoma suillum PS

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate Dsui_1048 Dsui_1048 glutamine synthetase, type I

Query= SwissProt::Q3V5W6
         (468 letters)



>FitnessBrowser__PS:Dsui_1048
          Length = 470

 Score =  670 bits (1728), Expect = 0.0
 Identities = 317/464 (68%), Positives = 381/464 (82%), Gaps = 1/464 (0%)

Query: 5   VQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGIEASD 64
           ++++K++DVK++D RFTDT+G + HV +P   A ++D FE G  FDGSSIAGWKGI+ASD
Sbjct: 8   MKMVKENDVKFVDFRFTDTRGKEQHVGVPV-SAFDEDKFESGHAFDGSSIAGWKGIQASD 66

Query: 65  MILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGIGDTV 124
           M+L+PD +TA +DPF ++ TLIL CD++EP+  +GYDRDPR+IA RAE YLK++GIGDT 
Sbjct: 67  MLLMPDPNTAYIDPFFDETTLILTCDVVEPADGKGYDRDPRSIAKRAEAYLKSSGIGDTA 126

Query: 125 FAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYFPVPP 184
           F GPEPEFFIFD V++K+D+SG+  KI+SE+ +W + +  +GGN GHRP VKGGYFPVPP
Sbjct: 127 FFGPEPEFFIFDSVEWKTDMSGTYVKIFSEEAAWSTAEKFDGGNAGHRPMVKGGYFPVPP 186

Query: 185 FDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKYVVHN 244
            D  +++R  MC  LE  G  VEVHHHEVATAGQNEIG  FNTLV++AD+ Q LKY+VHN
Sbjct: 187 VDSFNDMRAQMCLLLEACGVPVEVHHHEVATAGQNEIGTVFNTLVRRADQTQILKYIVHN 246

Query: 245 VADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGGIIKH 304
           VA  YG+TATFMPKP+ GDNGSGMHVH SI KDG+N FAG GYAGLSETALY+IGGIIKH
Sbjct: 247 VAHQYGKTATFMPKPIVGDNGSGMHVHQSIWKDGQNLFAGNGYAGLSETALYYIGGIIKH 306

Query: 305 GKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARFPDPA 364
            KALN  TNP TNSYKRLVP +EAPV LAYSA+NRSASIR+P+V S + RRIE RFPDP 
Sbjct: 307 AKALNAITNPGTNSYKRLVPHYEAPVKLAYSAKNRSASIRVPFVQSTKARRIETRFPDPI 366

Query: 365 ANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEELDKG 424
           ANPYL FAALLMAGLDGIQNKIHPGDAADKNLYDLPPEE  +IP VC SL EAL  LDK 
Sbjct: 367 ANPYLCFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEDAKIPTVCASLDEALANLDKD 426

Query: 425 RAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYSC 468
           R FLT+GGVFS+D+ID++I LK EE  K+R   HP+E++LYYSC
Sbjct: 427 REFLTRGGVFSNDWIDSFIDLKMEEVNKLRMTTHPVEFDLYYSC 470


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: 795
Number of extensions: 22
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: 470
Length adjustment: 33
Effective length of query: 435
Effective length of database: 437
Effective search space:   190095
Effective search space used:   190095
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 Dsui_1048 Dsui_1048 (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.24978.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.2e-207  673.7   0.0     7e-207  673.5   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_1048  Dsui_1048 glutamine synthetase, 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1048  Dsui_1048 glutamine synthetase, type I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  673.5   0.0    7e-207    7e-207       2     462 .]       6     469 ..       5     469 .. 0.99

  Alignments for each domain:
  == domain 1  score: 673.5 bits;  conditional E-value: 7e-207
                         TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvivPfr 78 
                                       +++k++ke++vkfvd+rf+D++Gk+++v +pvs+++e+ +e+g aFDgss+ G+k+i+ sD+ll+pdp+t+ i+Pf 
  lcl|FitnessBrowser__PS:Dsui_1048   6 DIMKMVKENDVKFVDFRFTDTRGKEQHVGVPVSAFDEDKFESGHAFDGSSIAGWKGIQASDMLLMPDPNTAYIDPFF 82 
                                       789************************************************************************** PP

                         TIGR00653  79 aekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflevdseege 154
                                       +e++l+++cdv ep++++ y+rdpRsiakrae +lk +++gd+++fGpE+EFf+fd+ve k+ ++ +++++ see++
  lcl|FitnessBrowser__PS:Dsui_1048  83 DETTLILTCDVVEPADGKGYDRDPRSIAKRAEAYLKsSGIGDTAFFGPEPEFFIFDSVEWKTDMSGTYVKIFSEEAA 159
                                       ************************************99*************************************** PP

                         TIGR00653 155 wn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEidikfdklvkaaDe 228
                                       w+  +++++gn g+++  kggYf+v+pvD+ +d+r +++l le+ g+ vev+HHEvata q+Ei++ f++lv+ aD+
  lcl|FitnessBrowser__PS:Dsui_1048 160 WStaEKFDGGNAGHRPMVKGGYFPVPPVDSFNDMRAQMCLLLEACGVPVEVHHHEVATAgQNEIGTVFNTLVRRADQ 236
                                       **87888999******************************************************************* PP

                         TIGR00653 229 ivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHakalaA 305
                                       ++++Ky+v+nva+++GktatFmpKp++gdngsGmHvh+s+wkdg+nlfag+  yagLsetalyyigGi+kHakal+A
  lcl|FitnessBrowser__PS:Dsui_1048 237 TQILKYIVHNVAHQYGKTATFMPKPIVGDNGSGMHVHQSIWKDGQNLFAGNG-YAGLSETALYYIGGIIKHAKALNA 312
                                       ***************************************************9.************************ PP

                         TIGR00653 306 ltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkid 382
                                       +tnp +nsYkRLvp yEAPv+laysaknRsa+iR+P ++++ka+RiE R+pDp anpYL+faallmAgldGi+nki+
  lcl|FitnessBrowser__PS:Dsui_1048 313 ITNPGTNSYKRLVPHYEAPVKLAYSAKNRSASIRVPFVQSTKARRIETRFPDPIANPYLCFAALLMAGLDGIQNKIH 389
                                       ***************************************************************************** PP

                         TIGR00653 383 pgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvEl 457
                                       pg++ dknly+l++ee ++  i+++ +sL+eal +l++d+  ++ ++v++++ i++fi+lk++Ev++lr++ hpvE+
  lcl|FitnessBrowser__PS:Dsui_1048 390 PGDAADKNLYDLPPEEDAK--IPTVCASLDEALANLDKDRefLTRGGVFSNDWIDSFIDLKMEEVNKLRMTTHPVEF 464
                                       *******************..*******************888999******************************* PP

                         TIGR00653 458 ekyld 462
                                         y++
  lcl|FitnessBrowser__PS:Dsui_1048 465 DLYYS 469
                                       ***95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (470 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.16
//
[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