Alignments for a candidate for asnB in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Pseudomonas simiae WCS417

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate GFF3757 PS417_19230 asparagine synthase

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__WCS417:GFF3757
          Length = 590

 Score =  262 bits (670), Expect = 3e-74
 Identities = 192/624 (30%), Positives = 297/624 (47%), Gaps = 52/624 (8%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  G       AQ AD    I+++   +  RGPD+ G+     +  G RRL I+D+ +
Sbjct: 1   MCGLAGELRFD--AQPADLAA-IERITHHLAPRGPDAWGFHAQGPIALGHRRLKIMDLSD 57

Query: 61  GG-QPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAAS 119
           G  QP+        + FNG IYN+ ELR+ELEA GY F +  DTEVLL  Y  + E    
Sbjct: 58  GSAQPMVDSQLGLSLAFNGAIYNFPELRQELEALGYAFYSGGDTEVLLKGYHAWGEALLP 117

Query: 120 KLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIE--ID 177
           KL GMFAF IW ++   L+ ARD  G+KPLY +    ++ FAS   +L+    DI   +D
Sbjct: 118 KLNGMFAFAIWERDAQRLFIARDRLGVKPLYLSRTGQRLRFASALPALLKG-GDINPILD 176

Query: 178 KEALQQYMSFQ-FVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTEEDK 236
             AL  Y++F   VP P TL A ++K+ P S   I   G    KT++   + P + E++ 
Sbjct: 177 PVALNHYLNFHAVVPAPRTLLAGIEKLPPASWMRIDASGKTEQKTWWTLPYGPHEDEKNL 236

Query: 237 LVKEVRDAIYDS----VNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFH-PSLKTFSVGFE 291
            +++  D + DS    V +  R+ V VG  LSGG+DSS +V + +E     L TFS+GFE
Sbjct: 237 TLEDWTDRVLDSTREAVAIRQRAAVDVGVLLSGGVDSSMLVGLLREVGVQDLSTFSIGFE 296

Query: 292 QQG---FSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFV 348
             G    +E   +   A   G  +    I+  E + +LP       +P+     I  Y +
Sbjct: 297 DAGGEAGNEFQYSDLIAKHYGTRHHQLRIAESEIIEQLPAAFRAMSEPMVSHDCIAFYLL 356

Query: 349 AKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGMRG 408
           ++E  KH  V  SG+GADELF GY+ Y +                      A  P     
Sbjct: 357 SREVAKHCKVVQSGQGADELFAGYHWYPQV-------------------DGASDPYAAYR 397

Query: 409 KSLLERGCTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSDINKM 468
            +  +R               +++       K    N +  D  + +F    + + ++K 
Sbjct: 398 DAFFDRS--------------YDDYAATVAPKWLTANDAAGDFVREHFAMPGADAAVDKA 443

Query: 469 QYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYLLR 528
             +D    +  D + + D MTMA  LE R PFLD  + ++++++P + K  +G  K +L+
Sbjct: 444 LRLDSTVMLVDDPVKRVDNMTMAWGLEARTPFLDYRLVELSARVPGQFKLPDG-GKQVLK 502

Query: 529 KAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIHKDYVL-QLLED 587
           +AA  ++P  V++RKK  FPVP    L+ +   WVR ++ +   D  +    +L +LL D
Sbjct: 503 EAARRVIPSEVIDRKKGYFPVPGLKHLQGDTLNWVRELLLDPSQDRGLFNPTMLDRLLTD 562

Query: 588 HCADKAD-NSRKIWTVLIFMIWHS 610
                      K+W +    +W S
Sbjct: 563 PQGQLTPLRGSKLWQLAALNLWLS 586


Lambda     K      H
   0.319    0.136    0.403 

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: 902
Number of extensions: 37
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 632
Length of database: 590
Length adjustment: 37
Effective length of query: 595
Effective length of database: 553
Effective search space:   329035
Effective search space used:   329035
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate GFF3757 PS417_19230 (asparagine synthase)
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))

# 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/TIGR01536.hmm
# target sequence database:        /tmp/gapView.1454823.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01536  [M=517]
Accession:   TIGR01536
Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.1e-126  407.3   0.0     7e-126  407.1   0.0    1.0  1  FitnessBrowser__WCS417:GFF3757  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__WCS417:GFF3757  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.1   0.0    7e-126    7e-126       1     516 [.       2     520 ..       2     521 .. 0.89

  Alignments for each domain:
  == domain 1  score: 407.1 bits;  conditional E-value: 7e-126
                       TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.evvivfnG 77 
                                     Cg+ag +  +a+ + + +ai+++++ la RGPDa g++ +      +lghrRL i+dls+g aQP+ + +    + fnG
  FitnessBrowser__WCS417:GFF3757   2 CGLAGELRFDAQPA-DLAAIERITHHLAPRGPDAWGFHAQ---GPIALGHRRLKIMDLSDGsAQPMVDSQlGLSLAFNG 76 
                                     ********988655.579******************7655...9***************************99****** PP

                       TIGR01536  78 EIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYyaseqgk 156
                                      IYN+ eLr+ele+ Gy F +  DtEV+L+ y++wge+l+ +L+GmFAfa+w++ +++lf+aRDrlG+kPLY ++++++
  FitnessBrowser__WCS417:GFF3757  77 AIYNFPELRQELEALGYAFYSGGDTEVLLKGYHAWGEALLPKLNGMFAFAIWERDAQRLFIARDRLGVKPLYLSRTGQR 155
                                     ******************************************************************************* PP

                       TIGR01536 157 llfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkelepakal....dgeekleeywevekee....v 226
                                     l faS + all+  +i++ ld  al ++l ++ +vp ++tl +++++l+pa+ +    +g+++ +++w + +      +
  FitnessBrowser__WCS417:GFF3757 156 LRFASALPALLKGGDINPILDPVALNHYLNFHaVVPAPRTLLAGIEKLPPASWMridaSGKTEQKTWWTLPYGPhedeK 234
                                     ********************************999*****************99997666666667***9987744446 PP

                       TIGR01536 227 keseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfe..dskdldeskaarkva 303
                                     + ++e+ ++++ +  ++av+ r +a v vgvllSGG+DSs+++ ++++   +++ tFsigfe  + ++ +e ++   +a
  FitnessBrowser__WCS417:GFF3757 235 NLTLEDWTDRVLDSTREAVAIRQRAAVDVGVLLSGGVDSSMLVGLLREVGVQDLSTFSIGFEdaGGEAGNEFQYSDLIA 313
                                     667889999999*************************************99***********65566778888****** PP

                       TIGR01536 304 delgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeea 382
                                     ++ gt+h+++ i e e++++l+  ++a+ ep+  +++i  ylls+++ ++ +kVv sG+GaDElf+GY+++ +     a
  FitnessBrowser__WCS417:GFF3757 314 KHYGTRHHQLRIAESEIIEQLPAAFRAMSEPMVSHDCIAFYLLSREVAKH-CKVVQSGQGADELFAGYHWYPQVD--GA 389
                                     **************************************************.*********************974..44 PP

                       TIGR01536 383 lelpeaselaekklllqaklakeselke.llkakleeelkekeelkkelkeeseleellrldlelllsdl.lrakDrvs 459
                                        p+a   a++  + ++++ +  ++    + +  +++   ++e+++   ++ +++++lrld + +l d+ +++ D ++
  FitnessBrowser__WCS417:GFF3757 390 SD-PYA---AYRDAFFDRSYDDYAATVApKWLTANDAAGDFVREHFAMPGADAAVDKALRLDSTVMLVDDpVKRVDNMT 464
                                     44.332...333344444443333332202222334444455566666777799999999999988776626666**** PP

                       TIGR01536 460 mahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKea 516
                                     ma++lE+R PflD +lvel +++p + kl dg  K +L+eaa++++P+e+ +RkK  
  FitnessBrowser__WCS417:GFF3757 465 MAWGLEARTPFLDYRLVELSARVPGQFKLPDG-GKQVLKEAARRVIPSEVIDRKKGY 520
                                     ******************************98.799******************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (590 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 33.62
//
[ok]

This GapMind analysis is from Jul 25 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:

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