Alignments for a candidate for glnA in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Polaromonas naphthalenivorans CJ2

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_011802159.1 PNAP_RS13885 type I glutamate--ammonia ligase

Query= BRENDA::P0A1P6
         (469 letters)



>NCBI__GCF_000015505.1:WP_011802159.1
          Length = 471

 Score =  636 bits (1641), Expect = 0.0
 Identities = 300/464 (64%), Positives = 364/464 (78%)

Query: 6   VLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGINESD 65
           V+ M+ E+EVKFVD R TDT+GKE HVT+P    + + F  G  FDGSS  GWKGI  SD
Sbjct: 8   VMNMIKENEVKFVDFRLTDTRGKENHVTVPVSHFDEDKFISGHAFDGSSFAGWKGIEASD 67

Query: 66  MVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATGIADTV 125
           M LMPD +TA IDPFF ++TL + CD++EP   + YDRDPRSIAKRAE YL+A+G+ DT 
Sbjct: 68  MQLMPDPNTANIDPFFEETTLFMTCDVVEPSDGKAYDRDPRSIAKRAEAYLKASGLGDTA 127

Query: 126 LFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGYFPVPP 185
            FGPEPEFF+FD++R+   +SG+   ID+ E  WNS  K EGGN+GHRP VKGGYFPVPP
Sbjct: 128 YFGPEPEFFIFDNVRWNTDMSGTFFKIDEYEAPWNSGKKLEGGNRGHRPSVKGGYFPVPP 187

Query: 186 VDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKYVVHN 245
           VDS QD+R+EM L++E +G+ VE  HHEVA AGQNE+ TRF+T+ ++AD  Q+ KYVVHN
Sbjct: 188 VDSTQDMRAEMSLILESLGIPVEVFHHEVAGAGQNEIGTRFSTLVERADWTQVMKYVVHN 247

Query: 246 VAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIGGVIKH 305
           VA+ +GKTATFMPKP+ GDNGSGMH H S+ K+G NLF+GD YAGLS+ ALYY+GG+IKH
Sbjct: 248 VANAYGKTATFMPKPVVGDNGSGMHVHQSIWKDGKNLFAGDGYAGLSDFALYYVGGIIKH 307

Query: 306 AKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVRFPDPA 365
           A+A+NA+ NP TNSYKRLVPGYEAPV LAYSA+NRSASIRIP VA+PK RRIE RFPDP 
Sbjct: 308 ARALNAITNPGTNSYKRLVPGYEAPVKLAYSAKNRSASIRIPYVANPKGRRIEARFPDPL 367

Query: 366 ANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNALDLD 425
            NPYL FAAL+MAGLDG++NKIHPGEA  K+LY LPPEE   IP V  SL++AL+ LD D
Sbjct: 368 MNPYLGFAALMMAGLDGVENKIHPGEAATKDLYHLPPEEDALIPTVCHSLDQALDCLDAD 427

Query: 426 REFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469
           R FL  GGVFTD  +D YI L+  E  R+R   HP+EFE+YYS+
Sbjct: 428 RGFLTKGGVFTDTMLDGYIDLKMGEVTRLRQATHPIEFEMYYSL 471


Lambda     K      H
   0.318    0.136    0.401 

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: 734
Number of extensions: 27
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: 469
Length of database: 471
Length adjustment: 33
Effective length of query: 436
Effective length of database: 438
Effective search space:   190968
Effective search space used:   190968
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_011802159.1 PNAP_RS13885 (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.31587.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-199  648.8   0.0   2.5e-199  648.6   0.0    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011802159.1  PNAP_RS13885 type I glutamate--a


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011802159.1  PNAP_RS13885 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  648.6   0.0  2.5e-199  2.5e-199       2     462 .]       7     470 ..       6     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: 648.6 bits;  conditional E-value: 2.5e-199
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 
                                               +v++++ke++vkfvd+r +D++Gk+++v++pvs+++e+ + +g aFDgss+ G+k+ie sD+ l+pdp+
  lcl|NCBI__GCF_000015505.1:WP_011802159.1   7 DVMNMIKENEVKFVDFRLTDTRGKENHVTVPVSHFDEDKFISGHAFDGSSFAGWKGIEASDMQLMPDPN 75 
                                               6899***************************************************************** PP

                                 TIGR00653  71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138
                                               t+ i+Pf +e++l ++cdv ep +++ y+rdpRsiakrae +lk ++lgd++yfGpE+EFf+fd+v+ +
  lcl|NCBI__GCF_000015505.1:WP_011802159.1  76 TANIDPFFEETTLFMTCDVVEPSDGKAYDRDPRSIAKRAEAYLKaSGLGDTAYFGPEPEFFIFDNVRWN 144
                                               ********************************************9************************ PP

                                 TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205
                                               + ++ +f+++d+ e+ wn  ++ e+gn+g++++ kggYf+v+pvD+++d+r e+ l+le+lg+ vev H
  lcl|NCBI__GCF_000015505.1:WP_011802159.1 145 TDMSGTFFKIDEYEAPWNsgKKLEGGNRGHRPSVKGGYFPVPPVDSTQDMRAEMSLILESLGIPVEVFH 213
                                               *******************99************************************************ PP

                                 TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273
                                               HEva a q+Ei+++f++lv+ aD ++++Kyvv+nva+ +GktatFmpKp++gdngsGmHvh+s+wkdg+
  lcl|NCBI__GCF_000015505.1:WP_011802159.1 214 HEVAGAgQNEIGTRFSTLVERADWTQVMKYVVHNVANAYGKTATFMPKPVVGDNGSGMHVHQSIWKDGK 282
                                               ****999************************************************************** PP

                                 TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342
                                               nlfag+  yagLs+ alyy+gGi+kHa+al+A+tnp +nsYkRLvpGyEAPv+laysaknRsa+iRiP+
  lcl|NCBI__GCF_000015505.1:WP_011802159.1 283 NLFAGDG-YAGLSDFALYYVGGIIKHARALNAITNPGTNSYKRLVPGYEAPVKLAYSAKNRSASIRIPY 350
                                               ******9.************************************************************* PP

                                 TIGR00653 343 sanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411
                                               +anpk++RiE R+pDp  npYL faal+mAgldG++nki+pge+  k+ly+l++ee +   i+++ +sL
  lcl|NCBI__GCF_000015505.1:WP_011802159.1 351 VANPKGRRIEARFPDPLMNPYLGFAALMMAGLDGVENKIHPGEAATKDLYHLPPEEDAL--IPTVCHSL 417
                                               ********************************************************999..******** PP

                                 TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                               ++ald l++d+  +++++v+++ +++ +i+lk+ Ev +lr + hp+E+e+y++
  lcl|NCBI__GCF_000015505.1:WP_011802159.1 418 DQALDCLDADRgfLTKGGVFTDTMLDGYIDLKMGEVTRLRQATHPIEFEMYYS 470
                                               ***********999*************************************96 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: 7.51
//
[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