Alignments for a candidate for asnB in Hydrogenovibrio halophilus DSM 15072

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Hydrogenovibrio halophilus DSM 15072

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_019894569.1 A377_RS0102545 N-acetylglutaminylglutamine amidotransferase

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000384235.1:WP_019894569.1
          Length = 618

 Score =  275 bits (703), Expect = 4e-78
 Identities = 194/626 (30%), Positives = 311/626 (49%), Gaps = 66/626 (10%)

Query: 20  EELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVENGG-QPLSYEDETYWIIFNG 78
           E  +  M + +  RGPD  G +    VG G RRLSIID+ + G QP+   DE   ++FNG
Sbjct: 17  EATLAPMLEKLAKRGPDDGGIWLQNQVGLGHRRLSIIDLSDAGHQPMV--DEELTLVFNG 74

Query: 79  EIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASKLRGMFAFLIWNKNDHVLY 138
            IYNY+ LRE+L   G+ F + SDTEV+L  YR +  E  ++  GMFAF +W+ + H L 
Sbjct: 75  CIYNYVALREQLIELGHAFRSHSDTEVILKAYRQWGMECVTRFEGMFAFALWDDHQHQLM 134

Query: 139 GARDPFGIKPLYYTTINDQVYFASERKSLMVAQN-DIEIDKEAL-QQYMSFQFVPEPSTL 196
            ARD FGIKPLYY  +   V FAS  ++L+ A   +I++D   L  Q+     VP P T+
Sbjct: 135 LARDRFGIKPLYYAPVEGGVRFASNTQALLAAGGVNIDLDPVGLHHQFTLHGVVPAPHTV 194

Query: 197 DAHVKKVEPGSQFTIRPDGDITFKTYF--------------KANFKPVQTEEDKLVKEVR 242
              V+K+ PG   T+ PDG +  ++++              +       T+    V+ V 
Sbjct: 195 LKGVRKLAPGQWMTVNPDGQMYQRSWWHLKAERPGPDHPSSRLQALSGVTDHQAWVEAVH 254

Query: 243 DAIYDSVNVHM-RSDVPVGSFLSGGIDSSFIVSVAKEFH-PSLKTFSVGFE---QQGFSE 297
           D + ++V+  +  SDVPVG  LSGG+DSS IV++  E     ++TFS+GFE   ++  SE
Sbjct: 255 DTLKEAVHKRLTASDVPVGVLLSGGLDSSLIVALLDEAGVEDIRTFSIGFEDVPEEKGSE 314

Query: 298 VDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKKHVT 357
            D + +        +   +I  E  +  L + V    +P+    A+  Y ++++  K V 
Sbjct: 315 FDYSDQVVERFQTRHQKFLIPNEAVLPRLQEAVDAMSEPMFAQDAVAFYLLSEQVSKEVK 374

Query: 358 VALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGMRGKSLLERGCT 417
           V +SG+GADE+FGGY  Y  P   +  E++               PE     +       
Sbjct: 375 VVMSGQGADEVFGGYFWY--PQMAQAAEKLG--------------PEAQAVDAF------ 412

Query: 418 PLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSD----INKMQYVDI 473
                    A  + +    +  +  +P+   RDVT  +  +  S  D    I+++  +D 
Sbjct: 413 ---------APFYFDRDHAEWSEMIHPDYHIRDVTTEWVQDRLSEEDADTFIDQVLRLDA 463

Query: 474 HTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYLLRKAAEG 533
              +  D + + D MTMA  LE RVPFLD  + +VA   P E K ++   KYLL+  A G
Sbjct: 464 SHLIVDDPVKRVDNMTMAWGLEARVPFLDHSLVEVAMTAPPETKLQD--FKYLLKAVARG 521

Query: 534 IVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNII--QESQTDAYIHKDYVLQLLEDHCAD 591
            VP+ V++R K  FP+P   +++    + +R+++  + +Q       DY+ +LL +  AD
Sbjct: 522 RVPDSVIDRPKGYFPMPALKYVRGPFYDMMRSVLTSEVAQKRGLFQSDYIERLLAEPEAD 581

Query: 592 KA---DNSRKIWTVLIFMIWHSINIE 614
            +       K+W   +  +W   +++
Sbjct: 582 ASFTRIQGSKLWHAALLELWLQTHVD 607


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: 968
Number of extensions: 53
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: 618
Length adjustment: 37
Effective length of query: 595
Effective length of database: 581
Effective search space:   345695
Effective search space used:   345695
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_019894569.1 A377_RS0102545 (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.3274554.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-140  455.1   0.0   2.3e-140  454.9   0.0    1.0  1  NCBI__GCF_000384235.1:WP_019894569.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000384235.1:WP_019894569.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.9   0.0  2.3e-140  2.3e-140       1     516 [.       2     534 ..       2     535 .. 0.87

  Alignments for each domain:
  == domain 1  score: 454.9 bits;  conditional E-value: 2.3e-140
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnekevv 72 
                                           Cgi g +  + + ++ e++++ mle+la+RGPD+ g+w +   ++++lghrRL+iidls++ +QP+ +e+  +
  NCBI__GCF_000384235.1:WP_019894569.1   2 CGICGEIYWDGQKAS-EATLAPMLEKLAKRGPDDGGIWLQ---NQVGLGHRRLSIIDLSDAgHQPMVDEE-LT 69 
                                           9***98877666444.58**********************...79**************999*******9.79 PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           +vfnG IYN+ +Lre+l+e G+ F+++sDtEViL+ay++wg e+v r+eGmFAfalwd+++++l+laRDr+Gi
  NCBI__GCF_000384235.1:WP_019894569.1  70 LVFNGCIYNYVALREQLIELGHAFRSHSDTEVILKAYRQWGMECVTRFEGMFAFALWDDHQHQLMLARDRFGI 142
                                           ************************************************************************* PP

                             TIGR01536 146 kPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkelepakal....dgee 213
                                           kPLYya  +g + faS  +alla+  ++  ld  +l++++tl+ +vp ++t+ k+v++l p++ +    dg+ 
  NCBI__GCF_000384235.1:WP_019894569.1 143 KPLYYAPVEGGVRFASNTQALLAAGGVNIDLDPVGLHHQFTLHgVVPAPHTVLKGVRKLAPGQWMtvnpDGQM 215
                                           ******************************************99*******************9999666666 PP

                             TIGR01536 214 kleeywevekee..............vkeseeelveelrelledavkkrlv.advpvgvllSGGlDSslvaai 271
                                           + +++w+++ e+                ++ ++ ve + ++l++av+krl  +dvpvgvllSGGlDSsl++a+
  NCBI__GCF_000384235.1:WP_019894569.1 216 YQRSWWHLKAERpgpdhpssrlqalsGVTDHQAWVEAVHDTLKEAVHKRLTaSDVPVGVLLSGGLDSSLIVAL 288
                                           6666******999*********9998778899******************989******************** PP

                             TIGR01536 272 akkeaksevktFsigfe..dskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasip 342
                                           +++   ++++tFsigfe   +++ +e ++  +v++ + t+h+++li +e+vl  l+e + a+ ep+  ++++ 
  NCBI__GCF_000384235.1:WP_019894569.1 289 LDEAGVEDIRTFSIGFEdvPEEKGSEFDYSDQVVERFQTRHQKFLIPNEAVLPRLQEAVDAMSEPMFAQDAVA 361
                                           ***9999**********33344555666********************************************* PP

                             TIGR01536 343 lyllsklarekgvkVvLsGeGaDElfgGYeyfrea.kaeealelpeaselaekklllqaklakeselkellka 414
                                            ylls++++++ vkVv+sG+GaDE+fgGY ++ ++ +a+e+l  pea+ + + + ++ ++ +   e  e+++ 
  NCBI__GCF_000384235.1:WP_019894569.1 362 FYLLSEQVSKE-VKVVMSGQGADEVFGGYFWYPQMaQAAEKLG-PEAQAVDAFAPFYFDRDH--AEWSEMIHP 430
                                           **********9.********************98614444554.554443332222222222..222333333 PP

                             TIGR01536 415 kleeelkekeelkkelkee...seleellrldlelll.sdllrakDrvsmahslEvRvPflDkelvelalsip 483
                                           +++    ++e ++++l+ee   + ++++lrld+  l+  d +++ D ++ma++lE+RvPflD+ lve+a++ p
  NCBI__GCF_000384235.1:WP_019894569.1 431 DYHIRDVTTEWVQDRLSEEdadTFIDQVLRLDASHLIvDDPVKRVDNMTMAWGLEARVPFLDHSLVEVAMTAP 503
                                           33333333333333333333448999***9998766505567777**************************** PP

                             TIGR01536 484 pelklrdgkeKvlLreaaeellPeeileRkKea 516
                                           pe kl+d   K+lL+ +a++ +P+++ +R+K  
  NCBI__GCF_000384235.1:WP_019894569.1 504 PETKLQD--FKYLLKAVARGRVPDSVIDRPKGY 534
                                           *****86..79*******************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 26.21
//
[ok]

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