Alignments for a candidate for glnA in Dechloromonas agitata is5

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Dechloromonas agitata is5

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate WP_027457352.1 K420_RS0106405 type I glutamate--ammonia ligase

Query= SwissProt::Q3V5W6
         (468 letters)



>NCBI__GCF_000519045.1:WP_027457352.1
          Length = 471

 Score =  657 bits (1695), Expect = 0.0
 Identities = 318/465 (68%), Positives = 378/465 (81%), Gaps = 2/465 (0%)

Query: 5   VQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGIEASD 64
           ++++K++D K++D RFTDT+G + HVT+P   A ++D FE G  FDGSSIAGWKGI+ASD
Sbjct: 8   MKMVKENDAKFVDFRFTDTRGKEQHVTVPV-SAFDEDKFENGHAFDGSSIAGWKGIQASD 66

Query: 65  MILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGIGDTV 124
           M+L+PD DTA +DPF ++ T++L CD+++P+  +GYDRDPR+IA RAE YLK++GIGDT 
Sbjct: 67  MLLMPDPDTAYVDPFFDETTVVLSCDVVDPADGRGYDRDPRSIAKRAEAYLKSSGIGDTA 126

Query: 125 FAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEG-GNKGHRPGVKGGYFPVP 183
           + GPEPEFFIFD V++  D+SG   KI+S + +W S +  +G G  GHRP VKGGYFPVP
Sbjct: 127 YFGPEPEFFIFDGVEWNVDMSGCALKIHSAEAAWGSGEKNDGSGATGHRPTVKGGYFPVP 186

Query: 184 PFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKYVVH 243
           P D  H+IR+AM   LE +G  VEVHHHEVATAGQ EIG  FNTLVK+AD+ Q LKYVVH
Sbjct: 187 PVDSLHDIRSAMVLTLEALGCPVEVHHHEVATAGQCEIGTVFNTLVKRADQTQVLKYVVH 246

Query: 244 NVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGGIIK 303
           NVA  YG+TATFMPKP+ GDNGSGMHVH SI KDGKN FAG+GYAGLSE ALY+IGGIIK
Sbjct: 247 NVAHQYGKTATFMPKPIVGDNGSGMHVHQSIWKDGKNLFAGDGYAGLSELALYYIGGIIK 306

Query: 304 HGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARFPDP 363
           H KALN  TNP TNSYKRLVP +EAPV LAYSA+NRSASIRIP+V S + RRIEARFPDP
Sbjct: 307 HAKALNAITNPGTNSYKRLVPHYEAPVKLAYSAKNRSASIRIPFVASTKARRIEARFPDP 366

Query: 364 AANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEELDK 423
            ANPYL FAALLMAGLDGIQNKIHPGD A KNLYDLPPEE  +IP VC SL+EAL  LDK
Sbjct: 367 IANPYLCFAALLMAGLDGIQNKIHPGDPASKNLYDLPPEEDAQIPTVCASLEEALAALDK 426

Query: 424 GRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYSC 468
            R FLTKGGVFS+D+IDAY+ALK EE  +VR   HP+E++LYYSC
Sbjct: 427 DRDFLTKGGVFSNDWIDAYLALKMEEVNRVRMTTHPVEFDLYYSC 471


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: 27
Number of successful extensions: 3
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: 471
Length adjustment: 33
Effective length of query: 435
Effective length of database: 438
Effective search space:   190530
Effective search space used:   190530
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 WP_027457352.1 K420_RS0106405 (type I glutamate--ammonia ligase)
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.29881.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-204  664.4   0.0   4.6e-204  664.3   0.0    1.0  1  lcl|NCBI__GCF_000519045.1:WP_027457352.1  K420_RS0106405 type I glutamate-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000519045.1:WP_027457352.1  K420_RS0106405 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  664.3   0.0  4.6e-204  4.6e-204       2     462 .]       6     470 ..       5     470 .. 0.98

  Alignments for each domain:
  == domain 1  score: 664.3 bits;  conditional E-value: 4.6e-204
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 
                                               +v+k++ke++ kfvd+rf+D++Gk+++v++pvs+++e+ +e+g aFDgss+ G+k+i+ sD+ll+pdp+
  lcl|NCBI__GCF_000519045.1:WP_027457352.1   6 DVMKMVKENDAKFVDFRFTDTRGKEQHVTVPVSAFDEDKFENGHAFDGSSIAGWKGIQASDMLLMPDPD 74 
                                               789****************************************************************** PP

                                 TIGR00653  71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138
                                               t+ ++Pf +e+++++ cdv +p++++ y+rdpRsiakrae +lk +++gd++yfGpE+EFf+fd ve +
  lcl|NCBI__GCF_000519045.1:WP_027457352.1  75 TAYVDPFFDETTVVLSCDVVDPADGRGYDRDPRSIAKRAEAYLKsSGIGDTAYFGPEPEFFIFDGVEWN 143
                                               ********************************************99*********************** PP

                                 TIGR00653 139 easnssflevdseegewn...reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevs 204
                                                 ++   l+++s e++w+   ++  +g +g++++ kggYf+v+pvD+++dir+ +vl+le+lg  vev+
  lcl|NCBI__GCF_000519045.1:WP_027457352.1 144 VDMSGCALKIHSAEAAWGsgeKNDGSGATGHRPTVKGGYFPVPPVDSLHDIRSAMVLTLEALGCPVEVH 212
                                               *****************986444445599**************************************** PP

                                 TIGR00653 205 HHEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdg 272
                                               HHEvata q Ei++ f++lvk aD+++++Kyvv+nva+++GktatFmpKp++gdngsGmHvh+s+wkdg
  lcl|NCBI__GCF_000519045.1:WP_027457352.1 213 HHEVATAgQCEIGTVFNTLVKRADQTQVLKYVVHNVAHQYGKTATFMPKPIVGDNGSGMHVHQSIWKDG 281
                                               ********************************************************************* PP

                                 TIGR00653 273 enlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiP 341
                                               +nlfag+  yagLse alyyigGi+kHakal+A+tnp +nsYkRLvp yEAPv+laysaknRsa+iRiP
  lcl|NCBI__GCF_000519045.1:WP_027457352.1 282 KNLFAGDG-YAGLSELALYYIGGIIKHAKALNAITNPGTNSYKRLVPHYEAPVKLAYSAKNRSASIRIP 349
                                               *******9.************************************************************ PP

                                 TIGR00653 342 asanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpes 410
                                                +a++ka+RiE R+pDp anpYL+faallmAgldGi+nki+pg+p  knly+l++ee ++  i+++ +s
  lcl|NCBI__GCF_000519045.1:WP_027457352.1 350 FVASTKARRIEARFPDPIANPYLCFAALLMAGLDGIQNKIHPGDPASKNLYDLPPEEDAQ--IPTVCAS 416
                                               ************************************************************..******* PP

                                 TIGR00653 411 Leealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                               Leeal +l++d+  +++++v++++ i+a+++lk++Ev+++r++ hpvE+  y++
  lcl|NCBI__GCF_000519045.1:WP_027457352.1 417 LEEALAALDKDRdfLTKGGVFSNDWIDAYLALKMEEVNRVRMTTHPVEFDLYYS 470
                                               ************889999**********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (471 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: 8.88
//
[ok]

This GapMind analysis is from Apr 10 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