GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glnA in Phyllobacterium brassicacearum STM 196

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_106710730.1 CU102_RS08860 type I glutamate--ammonia ligase

Query= BRENDA::P0A1P6
         (469 letters)



>NCBI__GCF_003010955.1:WP_106710730.1
          Length = 469

 Score =  621 bits (1602), Expect = 0.0
 Identities = 298/468 (63%), Positives = 370/468 (79%), Gaps = 1/468 (0%)

Query: 2   SAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGI 61
           +A+ +L  + +++VKF+DLRFTD KGK QHVT+   +V+ + F +G MFDGSSI GWK I
Sbjct: 3   TAKDILKQIKDNDVKFLDLRFTDPKGKLQHVTMDVAEVDEDMFADGVMFDGSSIAGWKAI 62

Query: 62  NESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATGI 121
           NESDMVLMPD  T  +DPFFA ST++I CDIL+P + + Y+RDPR  AK+AE Y++A GI
Sbjct: 63  NESDMVLMPDTDTVHMDPFFAQSTMVILCDILDPISGEAYNRDPRGTAKKAEAYMKAEGI 122

Query: 122 ADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGYF 181
            DT+  GPE EFF+FDD+++ A    +   +D  E   N  T YE GN GHRP VKGGYF
Sbjct: 123 GDTIFVGPEAEFFVFDDVKYKADPYNTGFKLDSTELPSNDDTDYETGNLGHRPRVKGGYF 182

Query: 182 PVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKY 241
           PVPPVDSAQD+RSEM  V+ +MG+ VE HHHEVA A Q+E+  +F+ +T+ AD++ IYKY
Sbjct: 183 PVPPVDSAQDMRSEMLTVLTEMGVRVEKHHHEVAAA-QHELGIKFDALTRNADKMLIYKY 241

Query: 242 VVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIGG 301
           VVH VA+ +GKTATFMPKP+FGDNGSGMH HMS+ K G   F+G++YAGLSE  L++IGG
Sbjct: 242 VVHQVANAYGKTATFMPKPIFGDNGSGMHVHMSIWKEGKPTFAGNEYAGLSENCLFFIGG 301

Query: 302 VIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVRF 361
           +IKHAKAINA  NP+TNSYKRLVPGYEAPV+LAYSARNRSAS RIP  +SPK++R+E+RF
Sbjct: 302 IIKHAKAINAFTNPSTNSYKRLVPGYEAPVLLAYSARNRSASCRIPFGSSPKSKRVEIRF 361

Query: 362 PDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNA 421
           PDP ANPYL FAA+LMAGLDGIKNKIHPG+ MDK+LYDLP +E K+IP V GSL EAL +
Sbjct: 362 PDPTANPYLGFAAMLMAGLDGIKNKIHPGQPMDKDLYDLPAKELKKIPTVCGSLREALQS 421

Query: 422 LDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469
           LD DR FLKAGGVF D+ ID++I L+  E  R  MTPHPVE+++YYSV
Sbjct: 422 LDKDRGFLKAGGVFDDDQIDSFIELKMAEVMRFEMTPHPVEYDMYYSV 469


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: 753
Number of extensions: 25
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: 469
Length of database: 469
Length adjustment: 33
Effective length of query: 436
Effective length of database: 436
Effective search space:   190096
Effective search space used:   190096
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_106710730.1 CU102_RS08860 (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.3367942.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-203  662.6   0.0   1.7e-203  662.4   0.0    1.0  1  NCBI__GCF_003010955.1:WP_106710730.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106710730.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  662.4   0.0  1.7e-203  1.7e-203       2     462 .]       6     468 ..       5     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 662.4 bits;  conditional E-value: 1.7e-203
                             TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvi 74 
                                           ++lk +k+++vkf+dlrf+D kGkl++v++ v e++e+++ +g++FDgss+ G+k+i+esD++l+pd++t+ +
  NCBI__GCF_003010955.1:WP_106710730.1   6 DILKQIKDNDVKFLDLRFTDPKGKLQHVTMDVAEVDEDMFADGVMFDGSSIAGWKAINESDMVLMPDTDTVHM 78 
                                           68899******************************************************************** PP

                             TIGR00653  75 vPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssfl 146
                                           +Pf a++++++ cd+ +p+ +e y+rdpR +ak+ae ++k +++gd++++GpEaEFf+fd+v+ k    ++ +
  NCBI__GCF_003010955.1:WP_106710730.1  79 DPFFAQSTMVILCDILDPISGEAYNRDPRGTAKKAEAYMKaEGIGDTIFVGPEAEFFVFDDVKYKADPYNTGF 151
                                           ************************************************************************* PP

                             TIGR00653 147 evdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvataqaEidi 217
                                           ++ds+e   n  +++e+gn g++++ kggYf+v+pvD+a+d+r+e++++l+e+g++ve++HHEva aq+E++i
  NCBI__GCF_003010955.1:WP_106710730.1 152 KLDSTELPSNddTDYETGNLGHRPRVKGGYFPVPPVDSAQDMRSEMLTVLTEMGVRVEKHHHEVAAAQHELGI 224
                                           ******988878999********************************************************** PP

                             TIGR00653 218 kfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetal 290
                                           kfd l+++aD++++yKyvv++va+ +GktatFmpKp+fgdngsGmHvh+s+wk+g++ fag+e yagLse++l
  NCBI__GCF_003010955.1:WP_106710730.1 225 KFDALTRNADKMLIYKYVVHQVANAYGKTATFMPKPIFGDNGSGMHVHMSIWKEGKPTFAGNE-YAGLSENCL 296
                                           ***************************************************************.********* PP

                             TIGR00653 291 yyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpY 363
                                           ++igGi+kHaka++A+tnp++nsYkRLvpGyEAPv laysa+nRsa+ RiP  ++pk+kR+E+R+pDp+anpY
  NCBI__GCF_003010955.1:WP_106710730.1 297 FFIGGIIKHAKAINAFTNPSTNSYKRLVPGYEAPVLLAYSARNRSASCRIPFGSSPKSKRVEIRFPDPTANPY 369
                                           ************************************************************************* PP

                             TIGR00653 364 LafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeeli 434
                                           L faa+lmAgldGiknki+pg+p+dk+ly+l+ +elk+  i+++  sL+eal++l++d+  +++++v+ ++ i
  NCBI__GCF_003010955.1:WP_106710730.1 370 LGFAAMLMAGLDGIKNKIHPGQPMDKDLYDLPAKELKK--IPTVCGSLREALQSLDKDRgfLKAGGVFDDDQI 440
                                           **************************************..*******************9999********** PP

                             TIGR00653 435 eafielkrkEveelrlkvhpvElekyld 462
                                           ++fielk++Ev ++++++hpvE  +y++
  NCBI__GCF_003010955.1:WP_106710730.1 441 DSFIELKMAEVMRFEMTPHPVEYDMYYS 468
                                           **************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (469 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: 00:00:00.01
# Mc/sec: 13.97
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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