Alignments for a candidate for asnB in Thiohalomonas denitrificans HLD2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Thiohalomonas denitrificans HLD2

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_092994041.1 BLP65_RS06145 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_900102855.1:WP_092994041.1
          Length = 659

 Score =  290 bits (741), Expect = 2e-82
 Identities = 190/605 (31%), Positives = 311/605 (51%), Gaps = 34/605 (5%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  G+ N    A      EL   M   + HRGPD         VG    RLSIID+E 
Sbjct: 1   MCGIAGILNLRRGAPAVGSLEL-GAMIAPLAHRGPDGADVRRFGPVGLAHARLSIIDLEG 59

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QPL+ ED + W++ NGEI+N+ ELR++L++ G++F T+SDTEV++  Y  + E    +
Sbjct: 60  GKQPLANEDGSIWVVLNGEIFNFPELRQQLKSAGHSFRTESDTEVIVHLYEDHGEAFVHQ 119

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDI-EIDKE 179
           L G FA  +W+     L   RD  GI PL+Y+   ++++FASE K++   Q      + E
Sbjct: 120 LNGQFAIALWDSVQEKLVLVRDRVGIAPLFYSEEGERLFFASEVKAIQPVQKRTPRANLE 179

Query: 180 ALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQT----EED 235
           AL+Q M++     P+TL   V ++ PG   T+  +G ++   Y+  ++    T     E+
Sbjct: 180 ALEQVMTYWAPLSPNTLFEGVHELPPGHLMTVE-NGKMSLHRYWDWSYPSDGTYDERNEE 238

Query: 236 KLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPS-LKTFSVGFEQQG 294
           +L +E+R  + D+V + +RSDVPVG++LSGG+DSS I ++ ++   + LKTFS+GF+Q+G
Sbjct: 239 ELAEELRSLLADAVRIRLRSDVPVGAYLSGGLDSSAIAALIRQADSAPLKTFSIGFDQEG 298

Query: 295 FSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKK 354
           + E D   E  + LG  + S      +     P+ +WH + PL   A  P+  ++   + 
Sbjct: 299 YDESDYQAEMVSHLGTRHRSFQCGLSDISESFPETIWHAETPLLRTAPTPMKLLSGHVRD 358

Query: 355 H-VTVALSGEGADELFGGYNIYREPLSLKPFERIPSG------LKKMLLHVAAVMPEGMR 407
               V L+GEGADE+ GGY+I++E    + + R P        LK++  ++     + + 
Sbjct: 359 EGYKVVLTGEGADEVLGGYDIFKEAKIRQFWSRNPDSKFRPALLKRLYPYLNIAGGQSLA 418

Query: 408 G-KSLLERGCTPLQDRYIGNAK----------IFEESVKKQLLKHYNPNLSYRDVTKTYF 456
             K    RG       +  +             F E +++ +L  Y    S R +    F
Sbjct: 419 YLKQFFGRGLHEPDSPWFSHVPRWTTTGATKGFFSERMQEYVLSGYE---SARSLLPAEF 475

Query: 457 TESSSYSDINKMQYVDIHTWMRGDILL-KADKMTMANSLELRVPFLDKVVFDVASKIPDE 515
                +    K QY++  T M G +L  + D+M MAN +E R PFLD  + + A++I   
Sbjct: 476 DR---WHWFEKAQYIESKTLMAGYLLCSQGDRMLMANGVEGRYPFLDHRIIEFANRIHPR 532

Query: 516 LKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVP-IRHWLKNEMNEWVRNIIQESQTDA 574
           LK +  T KYLL+KA    +P+ +  R K  +  P    +L  ++ E++  +++  +   
Sbjct: 533 LKMRGLTEKYLLKKAVGRYLPKRIAERTKQPYRAPESAPFLNRQVPEFIHEMMKPEKLRD 592

Query: 575 YIHKD 579
           Y + D
Sbjct: 593 YGYFD 597


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: 1016
Number of extensions: 50
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 632
Length of database: 659
Length adjustment: 38
Effective length of query: 594
Effective length of database: 621
Effective search space:   368874
Effective search space used:   368874
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_092994041.1 BLP65_RS06145 (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.4060825.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-153  498.7   0.0   1.4e-153  498.5   0.0    1.0  1  NCBI__GCF_900102855.1:WP_092994041.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900102855.1:WP_092994041.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  498.5   0.0  1.4e-153  1.4e-153       1     517 []       2     564 ..       2     564 .. 0.90

  Alignments for each domain:
  == domain 1  score: 498.5 bits;  conditional E-value: 1.4e-153
                             TIGR01536   1 Cgiagivdlkakake.eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.ev 71 
                                           Cgiagi++l++ a    + ++ +m+  lahRGPD+  v    +   ++l+h+RL+iidl++g+QPl+ne+ + 
  NCBI__GCF_900102855.1:WP_092994041.1   2 CGIAGILNLRRGAPAvGSLELGAMIAPLAHRGPDGADV--R-RFGPVGLAHARLSIIDLEGGKQPLANEDgSI 71 
                                           *********99998888899****************95..3.569**************************** PP

                             TIGR01536  72 vivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlG 144
                                           ++v nGEI+N+ eLr++l+ +G++F+t+sDtEVi+++ye +ge++v++L+G+FA+alwd+ +++l+l+RDr+G
  NCBI__GCF_900102855.1:WP_092994041.1  72 WVVLNGEIFNFPELRQQLKSAGHSFRTESDTEVIVHLYEDHGEAFVHQLNGQFAIALWDSVQEKLVLVRDRVG 144
                                           ************************************************************************* PP

                             TIGR01536 145 ikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeek 214
                                           i PL+y++e+++l+faSE+Ka+ ++++ +++ + eal +++t++   +++tlf++v+el+p++ +   +g+ +
  NCBI__GCF_900102855.1:WP_092994041.1 145 IAPLFYSEEGERLFFASEVKAIQPVQKRTPRANLEALEQVMTYWAPLSPNTLFEGVHELPPGHLMtveNGKMS 217
                                           ********************************************9999****************998888889 PP

                             TIGR01536 215 leeywevekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktF 283
                                           l++yw+ ++++     + +eeel eelr+ll dav+ rl++dvpvg++lSGGlDSs++aa++++   +++ktF
  NCBI__GCF_900102855.1:WP_092994041.1 218 LHRYWDWSYPSdgtyDERNEEELAEELRSLLADAVRIRLRSDVPVGAYLSGGLDSSAIAALIRQADSAPLKTF 290
                                           999******999998888999********************************************99****** PP

                             TIGR01536 284 sigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvk 356
                                           sigf+ ++ +des+++++++ +lgt+h++++    ++ + ++e i++ e p+  +a +p+ lls  +r++g+k
  NCBI__GCF_900102855.1:WP_092994041.1 291 SIGFD-QEGYDESDYQAEMVSHLGTRHRSFQCGLSDISESFPETIWHAETPLLRTAPTPMKLLSGHVRDEGYK 362
                                           *****.******************************************************************* PP

                             TIGR01536 357 VvLsGeGaDElfgGYeyfreakaeeale..............................lpeaselaekkl... 396
                                           VvL+GeGaDE++gGY++f+eak ++ +                                          +   
  NCBI__GCF_900102855.1:WP_092994041.1 363 VVLTGEGADEVLGGYDIFKEAKIRQFWSrnpdskfrpallkrlypylniaggqslaylK----------Qffg 425
                                           ***************************99999999888888887776655555533330..........1345 PP

                             TIGR01536 397 ...........llqaklakeselkellkakleeelke.....keelkkelkeeseleellrldlelllsdllr 453
                                                       +  +++++ ++k +++++++e + +     ++ l +e+ + + +e++++ + ++l+ ++l+
  NCBI__GCF_900102855.1:WP_092994041.1 426 rglhepdspwfSHVPRWTTTGATKGFFSERMQEYVLSgyesaRSLLPAEFDRWHWFEKAQYIESKTLMAGYLL 498
                                           5555666666644455555555555555555544433000003334444444499****************** PP

                             TIGR01536 454 ak..DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                            +  Dr++ma+++E R+PflD++++e+a +i p lk+r  +eK+lL++a+ ++lP++i+eR K+++
  NCBI__GCF_900102855.1:WP_092994041.1 499 CSqgDRMLMANGVEGRYPFLDHRIIEFANRIHPRLKMRGLTEKYLLKKAVGRYLPKRIAERTKQPY 564
                                           999************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (659 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: 00:00:00.01
# Mc/sec: 21.34
//
[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