Alignments for a candidate for asnB in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Halomonas desiderata SP1

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_086508878.1 BZY95_RS05010 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_002151265.1:WP_086508878.1
          Length = 631

 Score =  296 bits (758), Expect = 2e-84
 Identities = 200/640 (31%), Positives = 337/640 (52%), Gaps = 46/640 (7%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDE----HVGFGFRRLSII 56
           MCG  G  +   ++      + IK M  ++ HRGPD  G F+ +    HVG G RRLSI+
Sbjct: 1   MCGISGFIDWKNISGL----DCIKAMTDVLHHRGPDDSGLFYKQYEGAHVGLGHRRLSIL 56

Query: 57  DVENGG-QPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKE 115
           D+ + G QP+ +   T  I++NGE+YN+ E+R ELE +GY F++ SDTEV+L  Y  +  
Sbjct: 57  DLSSHGHQPMDHRHLT--IVYNGEVYNFKEIRTELERQGYVFDSGSDTEVILKAYHCWGI 114

Query: 116 EAASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSL-MVAQNDI 174
           E   +L GMFA  I++     L   RD  G+KPLY+   +    FASE KS         
Sbjct: 115 EMVHRLNGMFALAIFDAEKKELVLLRDRAGVKPLYWYYHDGLFLFASELKSFHQHPAFKK 174

Query: 175 EIDKEALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPD-GDITFKTYFKA-NF--KP- 229
           E+  + L  ++ + ++P+P ++  H +K++ G+  TI  D      K Y+   +F  KP 
Sbjct: 175 ELCLDGLALFLQYGYIPQPHSIFKHTQKLKAGNSLTINLDQRSFEEKKYWDVLDFYRKPK 234

Query: 230 VQTEEDKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFH-PSLKTFSV 288
           ++  E++ ++E    +  +    M +DVPVG FLSGG DSS + ++ +      LKTF++
Sbjct: 235 LKVSEEEALRETERLLTSACEYRMVADVPVGVFLSGGYDSSAVTALLQSHRSEKLKTFAI 294

Query: 289 GFEQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFV 348
           GF ++ ++E   A+  A  LG ++     + ++ ++ LP++   +D+P  D + IP   V
Sbjct: 295 GFHEEAYNEAHHARRVAEHLGTDHTEYYCTHQDALDILPRLPEIWDEPFGDASTIPTVLV 354

Query: 349 AKEAKKHVTVALSGEGADELFGGYNIYREPLSLKP-FERIP---------SGLKKMLLHV 398
           ++ A+K VTV+LS +G DE+FGGY+ Y     ++  F R+P         S +K   +  
Sbjct: 355 SELARKQVTVSLSADGGDEIFGGYDKYIYAKKMESIFGRVPFRNQFGRFLSSIKPGSIPF 414

Query: 399 AAVMPEGMRG----KSLLERGCTPLQDRYIGNAKI---FEESVKKQLLKHYNPNLSYRDV 451
            +  P   R      S LE   +      IG+A      EE + K ++       SY  +
Sbjct: 415 LSRDPIFSRRYAKVASSLEAKHSTEMLGIIGSAFFRAEVEELIAKPIVHLATDFESYEGL 474

Query: 452 TKTYFTESSSYSDI-NKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVAS 510
                     ++D+ N +  VD  T+   DIL+K D+ TM+ SLE R P LD  + +  +
Sbjct: 475 --------DEFNDLYNSLMAVDYKTYQLDDILVKVDRATMSCSLEGREPLLDYRIIEYVA 526

Query: 511 KIPDELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQES 570
           ++   LK +    KYLL+K     +P+ +++R K+GF VPI  W + E+ +++ + + ES
Sbjct: 527 RLESSLKIRGDERKYLLKKITHQYLPKEMMDRPKMGFGVPILDWFRAELRDYLLSYLSES 586

Query: 571 Q--TDAYIHKDYVLQLLEDHCADKADNSRKIWTVLIFMIW 608
           +       + + V+++ +++   K D+  KIW +L+F +W
Sbjct: 587 RLAEAGIFNVNKVIEVRDEYLNGKNDDISKIWFLLVFEMW 626


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: 1010
Number of extensions: 52
Number of successful extensions: 7
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: 631
Length adjustment: 38
Effective length of query: 594
Effective length of database: 593
Effective search space:   352242
Effective search space used:   352242
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: 54 (25.4 bits)

Align candidate WP_086508878.1 BZY95_RS05010 (asparagine synthase (glutamine-hydrolyzing))
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.10806.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-146  474.8   0.0   2.6e-146  474.6   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086508878.1  BZY95_RS05010 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508878.1  BZY95_RS05010 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.6   0.0  2.6e-146  2.6e-146       1     517 []       2     563 ..       2     563 .. 0.88

  Alignments for each domain:
  == domain 1  score: 474.6 bits;  conditional E-value: 2.6e-146
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkde.keenailghrRLaiidlseg.aQPlsn 67 
                                               Cgi g++d k+   +  + ik+m+++l+hRGPD++g++ ++ + ++++lghrRL+i dls+  +QP+  
  lcl|NCBI__GCF_002151265.1:WP_086508878.1   2 CGISGFIDWKNI--SGLDCIKAMTDVLHHRGPDDSGLFYKQyEGAHVGLGHRRLSILDLSSHgHQPMDH 68 
                                               ********9664..45689*********************99*****************9988*****9 PP

                                 TIGR01536  68 ekevvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgel 136
                                               ++  +iv+nGE+YN++e+r ele++Gy F + sDtEViL+ay+ wg e+v+rL+GmFA+a++d++k+el
  lcl|NCBI__GCF_002151265.1:WP_086508878.1  69 RH-LTIVYNGEVYNFKEIRTELERQGYVFDSGSDTEVILKAYHCWGIEMVHRLNGMFALAIFDAEKKEL 136
                                               99.79**************************************************************** PP

                                 TIGR01536 137 flaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelep 205
                                               +l RDr G+kPLY ++++g +lfaSE+K++ +++++k+el  ++la +l++ + p+++++fk+ ++l++
  lcl|NCBI__GCF_002151265.1:WP_086508878.1 137 VLLRDRAGVKPLYWYYHDGLFLFASELKSFHQHPAFKKELCLDGLALFLQYGYIPQPHSIFKHTQKLKA 205
                                               ****************************************************99*************** PP

                                 TIGR01536 206 akal.....dgeeklee..ywevekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGl 263
                                               +++l     +  +++ee  yw+v +       k seee+ +e+++ll+ a + r+vadvpvgv+lSGG 
  lcl|NCBI__GCF_002151265.1:WP_086508878.1 206 GNSLtinldQ--RSFEEkkYWDVLDFYrkpkLKVSEEEALRETERLLTSACEYRMVADVPVGVFLSGGY 272
                                               ****987543..3333356**9854333445999*********************************** PP

                                 TIGR01536 264 DSslvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilale 332
                                               DSs+v+a+++ +  +++ktF+igf+ +++++e+++ar+va++lgt+h+e++ +++++l+ l+++  +++
  lcl|NCBI__GCF_002151265.1:WP_086508878.1 273 DSSAVTALLQSHRSEKLKTFAIGFH-EEAYNEAHHARRVAEHLGTDHTEYYCTHQDALDILPRLPEIWD 340
                                               *************************.9****************************************** PP

                                 TIGR01536 333 eptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale................. 384
                                               ep+ +++ ip+ l+s+lar++ v+V Ls +G+DE+fgGY+++  ak+ e +                  
  lcl|NCBI__GCF_002151265.1:WP_086508878.1 341 EPFGDASTIPTVLVSELARKQ-VTVSLSADGGDEIFGGYDKYIYAKKMESIFgrvpfrnqfgrflssik 408
                                               *********************.*********************99888887779999999999888888 PP

                                 TIGR01536 385 ................lpeaselaekkl..............llqaklakeselkellkakleeelkek 423
                                                               +++        +              ++ + ++++   +el+ + + +  + +
  lcl|NCBI__GCF_002151265.1:WP_086508878.1 409 pgsipflsrdpifsrrYAK--------VassleakhstemlgIIGSAFFRAE-VEELIAKPIVHLATDF 468
                                               8887766666555444222........1222222223334543333333332.2333333444444444 PP

                                 TIGR01536 424 eelkkelkeeseleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdg 491
                                               e+ ++  + +   ++l+  d +++  d++++k Dr++m  slE R P+lD +++e++++++ +lk+r  
  lcl|NCBI__GCF_002151265.1:WP_086508878.1 469 ESYEGLDEFNDLYNSLMAVDYKTYQLDDILVKvDRATMSCSLEGREPLLDYRIIEYVARLESSLKIRGD 537
                                               44444444459999******************************************************* PP

                                 TIGR01536 492 keKvlLreaaeellPeeileRkKeaf 517
                                               ++K+lL+++ +++lP+e+++R+K++f
  lcl|NCBI__GCF_002151265.1:WP_086508878.1 538 ERKYLLKKITHQYLPKEMMDRPKMGF 563
                                               ************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (631 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.20
//
[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