Alignments for a candidate for asnB in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Pseudomonas fluorescens FW300-N1B4

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate Pf1N1B4_374 Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4)

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_374
          Length = 590

 Score =  261 bits (668), Expect = 5e-74
 Identities = 194/626 (30%), Positives = 299/626 (47%), Gaps = 56/626 (8%)

Query: 1   MCGFVGV--FNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDV 58
           MCG  G   F+  P    A     I+++   +  RGPD+ G+     +  G RRL I+D+
Sbjct: 1   MCGLAGELRFDHQPADLAA-----IERITHHLAPRGPDAWGFHSQGPIALGHRRLKIMDL 55

Query: 59  ENGG-QPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEA 117
            +G  QP+        + FNG IYN+ ELR ELE+ GY F +  DTEVLL  Y  + E  
Sbjct: 56  SDGSAQPMIDNQLGLSLAFNGAIYNFPELRTELESLGYAFYSGGDTEVLLKGYHAWGEAL 115

Query: 118 ASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIE-- 175
             KL GMFAF IW ++   L+ ARD  G+KPLY +    ++ FAS   +L+    DI   
Sbjct: 116 LPKLNGMFAFAIWERDAKRLFIARDRLGVKPLYLSRTGQRLRFASALPALLKG-GDINPI 174

Query: 176 IDKEALQQYMSFQ-FVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTEE 234
           +D+ AL  Y++F   VP P TL A ++K+ P S   I  DG    KT++   + P   E 
Sbjct: 175 LDQVALNHYLNFHAVVPAPRTLLAGIEKLPPASWMRIDVDGTTEQKTWWTLPYGPNADEL 234

Query: 235 DKLVKEVRDAIYDS----VNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFH-PSLKTFSVG 289
           +  +++ RD + DS    V +  R+ V VG  LSGG+DSS +V + +E     L TFS+G
Sbjct: 235 NLTLEDWRDRVLDSTRDAVAIRQRAAVDVGVLLSGGVDSSLLVGLLREVGVEDLSTFSIG 294

Query: 290 FEQQG---FSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLY 346
           F+  G     E   +   A   G  +    I  +E + +LP       +P+     I  Y
Sbjct: 295 FQDAGGERGDEFQYSDLIAKHYGTHHHQLRIDEKEIIEQLPAAFRAMSEPMVSHDCIAFY 354

Query: 347 FVAKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGM 406
            +++E  KH  V  SG+GADELF GY+ Y +                      A  P   
Sbjct: 355 LLSREVAKHCKVVQSGQGADELFAGYHWYPQV-------------------DGASDPYAA 395

Query: 407 RGKSLLERGCTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSDIN 466
              +  +R  T            +  +V+ + L     N +  D  K +F    + + ++
Sbjct: 396 YRDAFFDRSYTD-----------YAATVQPKWL---TANDAAGDFVKEHFARPGAEAAVD 441

Query: 467 KMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYL 526
           K   +D    +  D + + D MTMA  LE R PFLD  + ++++++P + K  +G  K +
Sbjct: 442 KALRLDSTVMLVDDPVKRVDNMTMAWGLEARTPFLDYRLVELSARVPGKFKLPDG-GKQV 500

Query: 527 LRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIHKDYVL-QLL 585
           L++AA  ++P  V++RKK  FPVP    L+ +   WVR ++ +   D  +    +L +LL
Sbjct: 501 LKEAARLVIPSEVIDRKKGYFPVPGLKHLQGDTLNWVRELLLDPSQDRGLFNPAMLDRLL 560

Query: 586 EDHCADKAD-NSRKIWTVLIFMIWHS 610
            D           K+W +    +W S
Sbjct: 561 TDPQGQLTPLRGSKLWQLAALNLWLS 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: 908
Number of extensions: 42
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 Pf1N1B4_374 (Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4))
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.5281.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   5.7e-126  407.4   0.0   6.5e-126  407.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_374  Asparagine synthetase [glutamine


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_374  Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.2   0.0  6.5e-126  6.5e-126       1     516 [.       2     520 ..       2     521 .. 0.89

  Alignments for each domain:
  == domain 1  score: 407.2 bits;  conditional E-value: 6.5e-126
                                     TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQP 64 
                                                   Cg+ag +  +++ + + +ai+++++ la RGPDa g++++      +lghrRL i+dls+g aQP
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_374   2 CGLAGELRFDHQPA-DLAAIERITHHLAPRGPDAWGFHSQ---GPIALGHRRLKIMDLSDGsAQP 62 
                                                   9*****99988755.579******************6555...9********************* PP

                                     TIGR01536  65 lsnek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfal 128
                                                   + +++    + fnG IYN+ eLr ele  Gy F +  DtEV+L+ y++wge+l+ +L+GmFAfa+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_374  63 MIDNQlGLSLAFNGAIYNFPELRTELESLGYAFYSGGDTEVLLKGYHAWGEALLPKLNGMFAFAI 127
                                                   ******99********************************************************* PP

                                     TIGR01536 129 wdekkgelflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvpt 192
                                                   w++ +++lf+aRDrlG+kPLY ++++++l faS + all+  +i++ ld+ al ++l ++ +vp 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_374 128 WERDAKRLFIARDRLGVKPLYLSRTGQRLRFASALPALLKGGDINPILDQVALNHYLNFHaVVPA 192
                                                   ************************************************************999** PP

                                     TIGR01536 193 ektlfkevkelepakal....dgeekleeywevekee....vkeseeelveelrelledavkkrl 249
                                                   ++tl +++++l+pa+ +    dg+++ +++w + +       + ++e+  +++ +  +dav+ r 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_374 193 PRTLLAGIEKLPPASWMridvDGTTEQKTWWTLPYGPnadeLNLTLEDWRDRVLDSTRDAVAIRQ 257
                                                   ***************99998888888888***9988833335555667777777788999***** PP

                                     TIGR01536 250 vadvpvgvllSGGlDSslvaaiakkeaksevktFsigfe..dskdldeskaarkvadelgtehke 312
                                                   +a v vgvllSGG+DSsl++ ++++   +++ tFsigf+  + +  de ++   +a++ gt+h++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_374 258 RAAVDVGVLLSGGVDSSLLVGLLREVGVEDLSTFSIGFQdaGGERGDEFQYSDLIAKHYGTHHHQ 322
                                                   **************************999*********965567788889*************** PP

                                     TIGR01536 313 vliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfrea 377
                                                   + i+e+e++++l+  ++a+ ep+  +++i  ylls+++ ++ +kVv sG+GaDElf+GY+++ + 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_374 323 LRIDEKEIIEQLPAAFRAMSEPMVSHDCIAFYLLSREVAKH-CKVVQSGQGADELFAGYHWYPQV 386
                                                   *****************************************.*********************97 PP

                                     TIGR01536 378 kaeealelpeaselaekklllqaklakeselke.llkakleeelkekeelkkelkeeseleellr 441
                                                     + +    +    a++  + ++++++  ++ +  + +  +++   ++e++++  +e +++++lr
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_374 387 DGASDP---Y---AAYRDAFFDRSYTDYAATVQpKWLTANDAAGDFVKEHFARPGAEAAVDKALR 445
                                                   444444...3...33445555555555544444134444455556667777788888999***** PP

                                     TIGR01536 442 ldlelllsdl.lrakDrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeell 505
                                                   ld + +l d+ +++ D ++ma++lE+R PflD +lvel +++p + kl dg  K +L+eaa+ ++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_374 446 LDSTVMLVDDpVKRVDNMTMAWGLEARTPFLDYRLVELSARVPGKFKLPDG-GKQVLKEAARLVI 509
                                                   999988776626666**********************************98.799********** PP

                                     TIGR01536 506 PeeileRkKea 516
                                                   P+e+ +RkK  
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_374 510 PSEVIDRKKGY 520
                                                   ********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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.89
//
[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