Alignments for a candidate for asnB in Desulfovibrio oxyclinae DSM 11498

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Desulfovibrio oxyclinae DSM 11498

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_026167556.1 B149_RS0109935 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000375485.1:WP_026167556.1
          Length = 625

 Score =  288 bits (736), Expect = 7e-82
 Identities = 219/648 (33%), Positives = 315/648 (48%), Gaps = 46/648 (7%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG+  F+++ +G+        +  I R    + HRGPD+ G W+  DGA+G V  G  R
Sbjct: 1   MCGITGFISSGSGSD-------SHCIERMVESLSHRGPDQFGVWN--DGAAG-VALGHRR 50

Query: 61  LSIIDIAH-SHQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAI 119
           LSI+D++    QP+      A  RYV+V+NGE+YN+L LR+EL   H   F +  D E I
Sbjct: 51  LSILDLSPLGRQPM----VSACGRYVIVYNGEVYNHLTLRNEL---HSYPFKSSSDTETI 103

Query: 120 LAGYHHWGT-EVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKK 178
           LA    WG  + +++  GMFAF LWD  TR+L   RD  GIKPL+      G  V   + 
Sbjct: 104 LAAVSAWGVGKAIEKFVGMFAFGLWDKKTRKLTLVRDRLGIKPLYYGIAEDGAWVFGSE- 162

Query: 179 CLLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVIT 238
            L  L     +   ID  AL  +    Y+P P +++    +LE G    +  ++  P +T
Sbjct: 163 -LKALHRYPAYSPSIDRNALALFFRHNYIPAPYSIYEKTWKLEPGQMVVLGEEE--PEVT 219

Query: 239 RYF----VPRFAASPITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDSTAIA 294
           R++    V R         +D    +E+ ++L D+V   M +DV +GAFLSGGIDS+ I 
Sbjct: 220 RWWDIDAVWREGFDNPWQMSDHDAVNELESLLSDAVGIRMLSDVPLGAFLSGGIDSSTIV 279

Query: 295 ALAIRHNPRLI-TFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVWY 353
           AL  +     + TF+ GF    F+E   A A A+ +G  H    V++ + +  +P +   
Sbjct: 280 ALMQKQATSPVKTFSIGFHEAAFNEAKHARAVADHLGTDHTELYVTSGDLLDVVPSMPQC 339

Query: 354 LDEPVADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYREPLSLRPFDYLPKPLR 413
            DEP AD + +P + +++  R+ V V LSG+G DELF GY  Y           LP   R
Sbjct: 340 WDEPFADLSQIPTYILSKLTREQVTVSLSGDGGDELFSGYARYFYASKWDTLTKLPVAFR 399

Query: 414 RSMGKVSKPLPE------GMRGKSLLHRGSLTLEERYYGNARSFSGAQLR---EVLPGFR 464
           R +    K  P       G  G  L  R  L L  R +     +  +  +   E + G +
Sbjct: 400 RIIMGALKVSPPSLFKLLGSFGPKLRWRLDL-LGMREFCEFYRYILSHFKHPDEFVLGAQ 458

Query: 465 PDWTHTDVTAPVYAESAGWDPVARMQHIDLFTWLRGDILVKADKITMANSLELRVPFLDP 524
              T      PV +     D  A M   DL  +L GDIL K D+ +MA  LE RVP LD 
Sbjct: 459 EWPTPLTDGNPVMS-----DRFAYMALKDLQMYLPGDILTKVDRASMAVGLEARVPLLDH 513

Query: 525 EVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFPVPIRHWLRAGELLEW 584
            V   A+R P  +KI     K+ LR+ L   VP  ++ RPK+GF VPI  W+R  EL EW
Sbjct: 514 RVVEFAARTPVSSKIRVGEGKWLLRQVLYRHVPQKIVDRPKMGFGVPIEGWMR-NELREW 572

Query: 585 AYATVGSSQAGH--LVDIAAVYRMLDEHRCGSSDHSRRLWTMLIFMLW 630
               +          +D   V RM +E   G +D +  LW +L+F  W
Sbjct: 573 CEDMLSPEAIARQGFIDPKMVERMWNEFLGGETDWNYYLWDILMFQSW 620


Lambda     K      H
   0.323    0.138    0.428 

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: 1041
Number of extensions: 68
Number of successful extensions: 10
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: 652
Length of database: 625
Length adjustment: 38
Effective length of query: 614
Effective length of database: 587
Effective search space:   360418
Effective search space used:   360418
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)

Align candidate WP_026167556.1 B149_RS0109935 (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.1208329.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-150  486.5   0.0     8e-150  486.1   0.0    1.1  1  NCBI__GCF_000375485.1:WP_026167556.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000375485.1:WP_026167556.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.1   0.0    8e-150    8e-150       1     517 []       2     557 ..       2     557 .. 0.89

  Alignments for each domain:
  == domain 1  score: 486.1 bits;  conditional E-value: 8e-150
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.ev 71 
                                           Cgi+g++ +   +  +++ i++m+e l+hRGPD++gvw+d   ++++lghrRL+i dls   +QP+ ++  ++
  NCBI__GCF_000375485.1:WP_026167556.1   2 CGITGFISSGSGS--DSHCIERMVESLSHRGPDQFGVWND-GAAGVALGHRRLSILDLSPLgRQPMVSACgRY 71 
                                           ********97654..5589*********************.89****************999******999** PP

                             TIGR01536  72 vivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewg.eelverLeGmFAfalwdekkgelflaRDrl 143
                                           viv+nGE+YNh  Lr+el+   y F++ sDtE iLaa  +wg  +++e++ GmFAf lwd+k+++l l+RDrl
  NCBI__GCF_000375485.1:WP_026167556.1  72 VIVYNGEVYNHLTLRNELH--SYPFKSSSDTETILAAVSAWGvGKAIEKFVGMFAFGLWDKKTRKLTLVRDRL 142
                                           ******************9..48************************************************** PP

                             TIGR01536 144 GikPLYyase.qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dge 212
                                           GikPLYy++  +g+ +f+SE+Kal + ++  +++d++ala ++ +++ p + +++++  +lep++ +   ++e
  NCBI__GCF_000375485.1:WP_026167556.1 143 GIKPLYYGIAeDGAWVFGSELKALHRYPAYSPSIDRNALALFFRHNYIPAPYSIYEKTWKLEPGQMVvlgEEE 215
                                           ********9989******************************************************9888777 PP

                             TIGR01536 213 ekleeywevekee.......vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaks 278
                                            ++ ++w+++          +++s++++v+el++ll dav  r+ +dvp+g++lSGG+DSs+++a+++k+a s
  NCBI__GCF_000375485.1:WP_026167556.1 216 PEVTRWWDIDAVWregfdnpWQMSDHDAVNELESLLSDAVGIRMLSDVPLGAFLSGGIDSSTIVALMQKQATS 288
                                           77788999998777899999***************************************************** PP

                             TIGR01536 279 evktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklar 351
                                           +vktFsigf+ +++++e+k+ar+vad+lgt+h+e+++++ ++l+ ++ +   ++ep+a+ ++ip+y+lskl+r
  NCBI__GCF_000375485.1:WP_026167556.1 289 PVKTFSIGFH-EAAFNEAKHARAVADHLGTDHTELYVTSGDLLDVVPSMPQCWDEPFADLSQIPTYILSKLTR 360
                                           **********.************************************************************** PP

                             TIGR01536 352 ekgvkVvLsGeGaDElfgGYeyfreak.aeealelpease....laekkl......................l 397
                                           e+ v+V LsG+G+DElf GY++++ a  ++   +lp a +                                l
  NCBI__GCF_000375485.1:WP_026167556.1 361 EQ-VTVSLSGDGGDELFSGYARYFYASkWDTLTKLPVAFRriimG----AlkvsppslfkllgsfgpklrwrL 428
                                           **.*****************9998775155555555555544321....023345556667777777777753 PP

                             TIGR01536 398 lqaklakeselkellkakleeelkekeelkkelkee.........seleellrldlelllsdllrak.Drvsm 460
                                               +++ +e+ +++  ++++  + +   ++  ++           +++ +  +dl+ +l+++++ k Dr+sm
  NCBI__GCF_000375485.1:WP_026167556.1 429 DLLGMREFCEFYRYILSHFKHPDEFVLGAQE-WPTPltdgnpvmsDRFAYMALKDLQMYLPGDILTKvDRASM 500
                                           3334556666666666555544333322222.2221355677777999************************* PP

                             TIGR01536 461 ahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           a +lE+RvP+lD+++ve+a+++p++ k+r g+ K+lLr+++ +++P++i++R+K++f
  NCBI__GCF_000375485.1:WP_026167556.1 501 AVGLEARVPLLDHRVVEFAARTPVSSKIRVGEGKWLLRQVLYRHVPQKIVDRPKMGF 557
                                           *******************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (625 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: 21.39
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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