Alignments for a candidate for asnB in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Kyrpidia tusciae DSM 2912

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_013074756.1 BTUS_RS03560 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000092905.1:WP_013074756.1
          Length = 648

 Score =  577 bits (1487), Expect = e-169
 Identities = 300/618 (48%), Positives = 405/618 (65%), Gaps = 12/618 (1%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  G+ N+    +     E ++QM + I+HRGPD +G++    VGFGFRRLSIIDV  
Sbjct: 1   MCGICGIANRDGNVEM----ETLRQMAERIIHRGPDDEGFYLGSGVGFGFRRLSIIDVAG 56

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QP+S ED + W++FNGEIYNY  LR EL  +G+ F TD+DTEVL+  Y     +   +
Sbjct: 57  GHQPMSNEDGSIWVVFNGEIYNYKWLRRELVERGHQFRTDTDTEVLVHLYEEEGLDLVGR 116

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQN-DIEIDKE 179
           LRGMFAF IW++    L  ARD FGIKPLYYT   + + FASE KSL+     +  +  E
Sbjct: 117 LRGMFAFAIWDEPRRTLLLARDHFGIKPLYYTLTPEGLVFASEIKSLLAVPGIEARVKPE 176

Query: 180 ALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTEEDKLVK 239
           +L  Y++FQ+VP+P T+   +KK+ P  +   R +G+     Y++A F+PV       V 
Sbjct: 177 SLWNYLTFQYVPDPETMFEGIKKLPPAHRLIWR-EGEAKLGRYWEATFEPVDRPLPAFVD 235

Query: 240 EVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPSLKTFSVGFEQQG-FSEV 298
           EVR+ + +SV  HM SDVP G+FLS G+DSS IV++ KE    +KTF+VGFE  G  SE+
Sbjct: 236 EVREVLRESVRAHMNSDVPRGAFLSSGVDSSTIVALLKELE-QVKTFTVGFEGAGGMSEI 294

Query: 299 DVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKKHVTV 358
           + A+ETA  LG ++   VIS   Y   LP + +H D+P+ADP+AI LYFVA+ A   V V
Sbjct: 295 EYARETARILGTDHRDVVISANRYAEVLPDLAYHQDEPVADPSAIALYFVAELASSDVAV 354

Query: 359 ALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGMRGKSLLERGCTP 418
            LSGEGADELFGGY IYREPLSL+ F  +P G+++ L   A  +P GM+G+  L RG   
Sbjct: 355 VLSGEGADELFGGYTIYREPLSLRMFHFLPDGVRRGLGEWARGLPSGMKGRGFLLRGSRL 414

Query: 419 LQDRYIGNAKIFEESVKKQLLKHYNPNLSY---RDVTKTYFTESSSYSDINKMQYVDIHT 475
           L DR++GNA IF ++ K+  LK + P+  +   + VT+  +   +   ++ +MQ VDIHT
Sbjct: 415 LSDRFVGNANIFSDNEKRAFLK-WTPDGGFACVKVVTEPLYERFADMDEVTQMQLVDIHT 473

Query: 476 WMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYLLRKAAEGIV 535
           W+ GDIL+KADKMTMANSLELRVPFLD  VFDVA +IP  L+   GTTKY+LR+A   I+
Sbjct: 474 WLPGDILMKADKMTMANSLELRVPFLDVRVFDVARRIPTSLRLLEGTTKYVLREAVRDIL 533

Query: 536 PEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIHKDYVLQLLEDHCADKADN 595
           PE V  RKKLGFPVP R WL++E+ EW R  + +   D Y  + ++L  LEDH   + D 
Sbjct: 534 PEAVTRRKKLGFPVPTRRWLRDELYEWARERLSDKSVDEYFDRAWLLARLEDHRLGRGDY 593

Query: 596 SRKIWTVLIFMIWHSINI 613
           +RK+WTVL+F++WH I I
Sbjct: 594 ARKLWTVLMFLLWHDIYI 611


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: 1137
Number of extensions: 41
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 632
Length of database: 648
Length adjustment: 38
Effective length of query: 594
Effective length of database: 610
Effective search space:   362340
Effective search space used:   362340
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_013074756.1 BTUS_RS03560 (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.130853.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-170  554.2   0.0   2.1e-170  554.0   0.0    1.0  1  NCBI__GCF_000092905.1:WP_013074756.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092905.1:WP_013074756.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  554.0   0.0  2.1e-170  2.1e-170       1     517 []       2     545 ..       2     545 .. 0.97

  Alignments for each domain:
  == domain 1  score: 554.0 bits;  conditional E-value: 2.1e-170
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evv 72 
                                           Cgi gi +++ +   e e++++m+e++ hRGPD+eg++     +++++g+rRL+iid+ +g+QP+sne+ + +
  NCBI__GCF_000092905.1:WP_013074756.1   2 CGICGIANRDGN--VEMETLRQMAERIIHRGPDDEGFYLG---SGVGFGFRRLSIIDVAGGHQPMSNEDgSIW 69 
                                           *********885..4558********************99...8***************************** PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           +vfnGEIYN++ Lr+el e+G++F+t++DtEV++++yee g +lv rL+GmFAfa+wde +++l+laRD++Gi
  NCBI__GCF_000092905.1:WP_013074756.1  70 VVFNGEIYNYKWLRRELVERGHQFRTDTDTEVLVHLYEEEGLDLVGRLRGMFAFAIWDEPRRTLLLARDHFGI 142
                                           ************************************************************************* PP

                             TIGR01536 146 kPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekl 215
                                           kPLYy+ + + l+faSEiK+lla++ i+a+++ e l+++lt+q+vp+++t+f+++k+l+pa+ l   +ge+kl
  NCBI__GCF_000092905.1:WP_013074756.1 143 KPLYYTLTPEGLVFASEIKSLLAVPGIEARVKPESLWNYLTFQYVPDPETMFEGIKKLPPAHRLiwrEGEAKL 215
                                           ******************************************************************9999999 PP

                             TIGR01536 216 eeywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfe 288
                                            +ywe++ e v+  + ++v+e+re l+++v++++ +dvp g++lS+G+DSs+++a++k+  +  vktF++gfe
  NCBI__GCF_000092905.1:WP_013074756.1 216 GRYWEATFEPVDRPLPAFVDEVREVLRESVRAHMNSDVPRGAFLSSGVDSSTIVALLKELEQ--VKTFTVGFE 286
                                           99********************************************************9955..********* PP

                             TIGR01536 289 dskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsG 361
                                           +   ++e ++ar++a+ lgt+h+ v+is++ +++ l+++ ++++ep+a++++i ly++++la+ + v VvLsG
  NCBI__GCF_000092905.1:WP_013074756.1 287 GAGGMSEIEYARETARILGTDHRDVVISANRYAEVLPDLAYHQDEPVADPSAIALYFVAELASSD-VAVVLSG 358
                                           ****************************************************************9.******* PP

                             TIGR01536 362 eGaDElfgGYeyfreakaeeale..........................lpeaselaekklllqaklakesel 408
                                           eGaDElfgGY ++re+ + + ++                          l + s+l + +++ +a++++ +e+
  NCBI__GCF_000092905.1:WP_013074756.1 359 EGADELFGGYTIYREPLSLRMFHflpdgvrrglgewarglpsgmkgrgfLLRGSRLLSDRFVGNANIFSDNEK 431
                                           ********************************99999998888888887777777888999************ PP

                             TIGR01536 409 kellkakleeelkekeelkkelkee....seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelv 476
                                           + +lk++ + + + ++ +++ l e+     e+ +++  d++++l++++++k D+++ma+slE+RvPflD +++
  NCBI__GCF_000092905.1:WP_013074756.1 432 RAFLKWTPDGGFACVKVVTEPLYERfadmDEVTQMQLVDIHTWLPGDILMKaDKMTMANSLELRVPFLDVRVF 504
                                           ************9999999988887888899****************************************** PP

                             TIGR01536 477 elalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           ++a +ip++l+l +g++K++Lrea++++lPe++  RkK +f
  NCBI__GCF_000092905.1:WP_013074756.1 505 DVARRIPTSLRLLEGTTKYVLREAVRDILPEAVTRRKKLGF 545
                                           **************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (648 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: 23.17
//
[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