Alignments for a candidate for asnB in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Nitriliruptor alkaliphilus DSM 45188

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_052669880.1 NITAL_RS20840 N-acetylglutaminylglutamine amidotransferase

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000969705.1:WP_052669880.1
          Length = 618

 Score =  260 bits (665), Expect = 1e-73
 Identities = 211/625 (33%), Positives = 302/625 (48%), Gaps = 42/625 (6%)

Query: 24  SAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNRLSIIDI-AHSHQPLRWGPPEAPD 82
           +A+A+   LM  RGPD  G W A     G V FG  RLSIID+ +H +QP+     +A  
Sbjct: 18  AAVAKMMGLMTDRGPDAEGMWSA-----GPVAFGHRRLSIIDLTSHGNQPMH----DADL 68

Query: 83  RYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAILAGYHHWGTEVLQRLRGMFAFAL 142
              +VFNG IYNY +LR+ELR + G  F +  D E +L  YH WG   + RL+GMFAFA+
Sbjct: 69  GLTIVFNGCIYNYQQLREELRAERGYRFFSTSDTEVVLKAYHAWGDRFVDRLQGMFAFAI 128

Query: 143 WDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKKCLLDLVELVGFDTEIDHRALQHYT 202
            +  +   F  RD FGIKP ++         AS    L  LV   G DT ID  AL HY 
Sbjct: 129 HERDSGRTFLGRDRFGIKPFYLTEDGARLRFASS---LPALVAAGGVDTSIDPVALHHYL 185

Query: 203 VLQ-YVPEPETLHRGVRRLESGCFARIRADQLAPVITRYFVPRFAASPITND-NDQARYD 260
                VP P T+  GVR+L       I AD     +  Y+ P F   P   D +++   D
Sbjct: 186 SFHAVVPAPHTIVNGVRKLPPATTLAIEADGRREQV-EYWRPDFTRDPDRADWSERDWED 244

Query: 261 EITAVLEDSVAKHMRADVTVGAFLSGGIDST-AIAALAIRHNPRLITFTTGFEREGFSEI 319
            + A L  +V   + ADV VG  LSGG+DS+ A+  LA      L TF+ GFE  G  E 
Sbjct: 245 AVLASLRQAVEWRLVADVPVGVLLSGGLDSSLAVGLLAEAGQRHLATFSIGFESFGGEEG 304

Query: 320 DVAVAS---AEAIGARHIAKVVSADEFVAALPEIVWYLDEPVADPALVPLFFVAREARKH 376
           D    S   A   G  H    +  +  + AL + +  + EP+     V  F +++E  KH
Sbjct: 305 DEFKYSDVVAREFGTDHHQLRIDTERMLPALGDAIGAMSEPMVSHDAVAFFLLSQEVAKH 364

Query: 377 VKVVLSGEGADELFGGYTIYREPLSLRPFDYLPKPLRRSMGKVSKPLPEGMRGKSLLHRG 436
           VKVV SG+GADE+F GY  Y  P+     +  P  + RS     +P P+    + +L R 
Sbjct: 365 VKVVQSGQGADEVFAGYHWY-PPMQALSDELGPGVVSRS----GRPGPD----RDVLVRR 415

Query: 437 SLTLEERYYGNARSFSGAQLREVL-PGFRPDWTHTDVTAPVYAESAGWDPVARMQ-HIDL 494
           ++   + Y+         ++ +VL P  R +   +      +    G +    M   +D 
Sbjct: 416 AV---DAYHAAFFDRPHDEMAQVLRPEHRIERDVSRQLVEDHFRQPGAETATDMALRLDS 472

Query: 495 FTWLRGDILVKADKITMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEP 554
              L  D + + D +TMA  LE RVPFLD EV AVA+R+P   K+ +   K  L+ A   
Sbjct: 473 QIMLVDDPVKRVDNMTMAWGLEARVPFLDHEVLAVAARIPPELKLAQ-EGKGVLKEAARR 531

Query: 555 IVPAHVLHRPKLGFPVPIRHWLRAGELLEWAYATVGSSQAGH--LVDIAAVYRML-DEHR 611
           ++P  V+ RPK  FPVP    L+ G  L+     + + +A    L + A V  +L D + 
Sbjct: 532 VIPNEVIDRPKGYFPVPALKHLQ-GPYLDHVRDALSAPEARERGLYEPAYVDALLADPNA 590

Query: 612 CGSSDHSRRLWTMLIFMLW---HAI 633
             +     +LW + +  +W   HA+
Sbjct: 591 SLTPLRGNKLWQLALLEMWLQTHAV 615


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: 1073
Number of extensions: 72
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: 618
Length adjustment: 38
Effective length of query: 614
Effective length of database: 580
Effective search space:   356120
Effective search space used:   356120
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_052669880.1 NITAL_RS20840 (N-acetylglutaminylglutamine amidotransferase)
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.905.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-134  434.8   0.0   3.3e-134  434.6   0.0    1.0  1  lcl|NCBI__GCF_000969705.1:WP_052669880.1  NITAL_RS20840 N-acetylglutaminyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052669880.1  NITAL_RS20840 N-acetylglutaminylglutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.6   0.0  3.3e-134  3.3e-134       1     516 [.       2     544 ..       2     545 .. 0.87

  Alignments for each domain:
  == domain 1  score: 434.6 bits;  conditional E-value: 3.3e-134
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                               Cg+ g +  +  +  + +a+++m+ ++  RGPDaeg+w+      +++ghrRL+iidl +  +QP++++
  lcl|NCBI__GCF_000969705.1:WP_052669880.1   2 CGFSGELRFDGRSP-DVAAVAKMMGLMTDRGPDAEGMWSA---GPVAFGHRRLSIIDLTSHgNQPMHDA 66 
                                               89999999977644.5689*********************...8**************9888******* PP

                                 TIGR01536  69 k.evvivfnGEIYNheeLreele.ekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkge 135
                                               +   +ivfnG IYN+++Lreel+ e+Gy+F ++sDtEV+L+ay++wg ++v+rL+GmFAfa++++ +g+
  lcl|NCBI__GCF_000969705.1:WP_052669880.1  67 DlGLTIVFNGCIYNYQQLREELRaERGYRFFSTSDTEVVLKAYHAWGDRFVDRLQGMFAFAIHERDSGR 135
                                               **99******************8358******************************************* PP

                                 TIGR01536 136 lflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkel 203
                                                fl RDr+GikP+Y ++++ +l faS + al+a+  +++++d  al+++l+++ +vp ++t+ ++v++l
  lcl|NCBI__GCF_000969705.1:WP_052669880.1 136 TFLGRDRFGIKPFYLTEDGARLRFASSLPALVAAGGVDTSIDPVALHHYLSFHaVVPAPHTIVNGVRKL 204
                                               *****************************************************999************* PP

                                 TIGR01536 204 epakal....dgeekleeywevekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGlD 264
                                               +pa  l    dg ++  eyw+ + ++     + se++  + +   l++av+ rlvadvpvgvllSGGlD
  lcl|NCBI__GCF_000969705.1:WP_052669880.1 205 PPATTLaieaDGRREQVEYWRPDFTRdpdrADWSERDWEDAVLASLRQAVEWRLVADVPVGVLLSGGLD 273
                                               *****9996655555556***99988888888899999******************************* PP

                                 TIGR01536 265 SslvaaiakkeaksevktFsigfe..dskdldeskaarkvadelgtehkevliseeevlkeleevilal 331
                                               Ssl + ++++  ++++ tFsigfe  + ++ de k+   va+e+gt+h+++ i+ e +l +l + i a+
  lcl|NCBI__GCF_000969705.1:WP_052669880.1 274 SSLAVGLLAEAGQRHLATFSIGFEsfGGEEGDEFKYSDVVAREFGTDHHQLRIDTERMLPALGDAIGAM 342
                                               ************************888999999************************************ PP

                                 TIGR01536 332 eeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale....lpease...... 390
                                                ep+  ++++  +lls+++ ++ vkVv sG+GaDE+f+GY+++  ++a  +      +    +      
  lcl|NCBI__GCF_000969705.1:WP_052669880.1 343 SEPMVSHDAVAFFLLSQEVAKH-VKVVQSGQGADEVFAGYHWYPPMQALSDELgpgvV----Srsgrpg 406
                                               **********************.********************998876654435551....2233344 PP

                                 TIGR01536 391 ......laekkl....llqaklake..selkellkakleeelkekeelkkelkee....seleellrld 443
                                                     +         +++a ++++   e++++l+ + + e+  +++l ++  ++    ++++ +lrld
  lcl|NCBI__GCF_000969705.1:WP_052669880.1 407 pdrdvlV----RravdAYHAAFFDRphDEMAQVLRPEHRIERDVSRQLVEDHFRQpgaeTATDMALRLD 471
                                               4444332....0334444444444311344556665555555555555555555556658888888899 PP

                                 TIGR01536 444 lelllsdl.lrakDrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeile 511
                                                + +l d+ +++ D ++ma++lE+RvPflD+e++ +a++ippelkl  ++ K +L+eaa++++P+e+ +
  lcl|NCBI__GCF_000969705.1:WP_052669880.1 472 SQIMLVDDpVKRVDNMTMAWGLEARVPFLDHEVLAVAARIPPELKLA-QEGKGVLKEAARRVIPNEVID 539
                                               8887776626666********************************97.579****************** PP

                                 TIGR01536 512 RkKea 516
                                               R+K  
  lcl|NCBI__GCF_000969705.1:WP_052669880.1 540 RPKGY 544
                                               **965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (618 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: 8.22
//
[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