Alignments for a candidate for glnA in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Sphingomonas koreensis DSMZ 15582

Align glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate Ga0059261_3384 Ga0059261_3384 glutamine synthetase, type I

Query= CharProtDB::CH_024014
         (469 letters)



>FitnessBrowser__Korea:Ga0059261_3384
          Length = 470

 Score =  584 bits (1506), Expect = e-171
 Identities = 289/467 (61%), Positives = 348/467 (74%), Gaps = 1/467 (0%)

Query: 2   SAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGI 61
           +A  +L M+ E  ++++DLRFTD KGK QH+T+ A  +  +   +G MFDGSSI GWK I
Sbjct: 4   TAADILKMVEEQSIEWIDLRFTDPKGKWQHLTMVASILGEDELTDGLMFDGSSIEGWKAI 63

Query: 62  NESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTGI 121
           NESDM+L PD      DPF A   LI+ CDI+EP T + Y RDPRS AKR+E YL+S GI
Sbjct: 64  NESDMILKPDLDAVWTDPFSATPMLILVCDIVEPSTGELYARDPRSTAKRSEAYLQSLGI 123

Query: 122 ADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGYF 181
            DTV  GPE EFF+FDD+RF ++ S S+  +DDIE   NSS QYE GN GHRP  KGGYF
Sbjct: 124 GDTVYVGPEAEFFMFDDVRFENTYSSSYYQLDDIELPGNSSKQYESGNMGHRPRAKGGYF 183

Query: 182 PVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKY 241
           PV PVDSA DIR EM   M +MGL  + HHHEVA A Q+E+   + T+ + AD +QIYKY
Sbjct: 184 PVAPVDSAVDIRGEMVSTMLEMGLPCDKHHHEVAAA-QHELGLTYGTLVQTADRMQIYKY 242

Query: 242 VVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIGG 301
           VVH VAH +GKTATFMPKP+  DNGSGMH H S+   G  LFAG+ YAGLSE  LY+IGG
Sbjct: 243 VVHQVAHAYGKTATFMPKPIKEDNGSGMHTHFSIWDGGKPLFAGNGYAGLSEMCLYFIGG 302

Query: 302 VIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVRF 361
           VIKHAKA+NA  NP+TNSYKRLVPGYEAPV+LAYS+RNRSAS RIP  +  KA+R+E RF
Sbjct: 303 VIKHAKALNAFTNPSTNSYKRLVPGYEAPVLLAYSSRNRSASCRIPYGAGSKAKRVEFRF 362

Query: 362 PDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNE 421
           PD  ANPYLC+AALLMAGLDGI+NKIHPG+ MDKNLYDLPPEE  E+P V GSL EAL+ 
Sbjct: 363 PDALANPYLCYAALLMAGLDGIQNKIHPGDPMDKNLYDLPPEELAEVPTVCGSLREALDS 422

Query: 422 LDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYS 468
           L+ D +FL  G VF+ + I+AYI ++R +  R  MTP PVEF++YYS
Sbjct: 423 LEADMDFLLKGDVFSKDQIEAYIEIKRGDVARWEMTPSPVEFDMYYS 469


Lambda     K      H
   0.318    0.136    0.400 

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: 674
Number of extensions: 17
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: 470
Length adjustment: 33
Effective length of query: 436
Effective length of database: 437
Effective search space:   190532
Effective search space used:   190532
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 Ga0059261_3384 Ga0059261_3384 (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.25696.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-197  641.2   0.0     5e-197  641.1   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3384  Ga0059261_3384 glutamine synthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3384  Ga0059261_3384 glutamine synthetase, type I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  641.1   0.0    5e-197    5e-197       2     462 .]       7     469 ..       6     469 .. 0.99

  Alignments for each domain:
  == domain 1  score: 641.1 bits;  conditional E-value: 5e-197
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 
                                               ++lk+++e+ ++ +dlrf+D kGk++++++ +s l e+ l++g++FDgss+eG+k+i+esD++lkpd++
  lcl|FitnessBrowser__Korea:Ga0059261_3384   7 DILKMVEEQSIEWIDLRFTDPKGKWQHLTMVASILGEDELTDGLMFDGSSIEGWKAINESDMILKPDLD 75 
                                               6889***************************************************************** PP

                                 TIGR00653  71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138
                                               ++ ++Pf+a+++l+++cd+ ep t+e y rdpRs+akr e +l+  ++gd+vy+GpEaEFf+fd+v+f+
  lcl|FitnessBrowser__Korea:Ga0059261_3384  76 AVWTDPFSATPMLILVCDIVEPSTGELYARDPRSTAKRSEAYLQsLGIGDTVYVGPEAEFFMFDDVRFE 144
                                               ********************************************99*********************** PP

                                 TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205
                                               ++ +ss++++d++e   n  +++e+gn g++++ kggYf+v+pvD+a+dir e+v+++ e+gl  +++H
  lcl|FitnessBrowser__Korea:Ga0059261_3384 145 NTYSSSYYQLDDIELPGNssKQYESGNMGHRPRAKGGYFPVAPVDSAVDIRGEMVSTMLEMGLPCDKHH 213
                                               *************97777779************************************************ PP

                                 TIGR00653 206 HEvataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274
                                               HEva aq+E+++ + +lv++aD +++yKyvv++va+ +GktatFmpKp+  dngsGmH+h+s+w  g++
  lcl|FitnessBrowser__Korea:Ga0059261_3384 214 HEVAAAQHELGLTYGTLVQTADRMQIYKYVVHQVAHAYGKTATFMPKPIKEDNGSGMHTHFSIWDGGKP 282
                                               ********************************************************************* PP

                                 TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343
                                               lfag+  yagLse++ly+igG++kHakal+A+tnp++nsYkRLvpGyEAPv lays +nRsa+ RiP+ 
  lcl|FitnessBrowser__Korea:Ga0059261_3384 283 LFAGNG-YAGLSEMCLYFIGGVIKHAKALNAFTNPSTNSYKRLVPGYEAPVLLAYSSRNRSASCRIPYG 350
                                               *****9.************************************************************** PP

                                 TIGR00653 344 anpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLe 412
                                               a  kakR+E+R+pD+ anpYL++aallmAgldGi+nki+pg+p+dknly+l++eel+e  ++++  sL+
  lcl|FitnessBrowser__Korea:Ga0059261_3384 351 AGSKAKRVEFRFPDALANPYLCYAALLMAGLDGIQNKIHPGDPMDKNLYDLPPEELAE--VPTVCGSLR 417
                                               **********************************************************..********* PP

                                 TIGR00653 413 ealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                               eald+le+d   +++++v++++ iea+ie+kr +v ++++++ pvE+ +y++
  lcl|FitnessBrowser__Korea:Ga0059261_3384 418 EALDSLEADMdfLLKGDVFSKDQIEAYIEIKRGDVARWEMTPSPVEFDMYYS 469
                                               *********988999***********************************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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.69
//
[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