Alignments for a candidate for asnB in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Pseudomonas simiae WCS417

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate GFF2243 PS417_11435 asparagine synthase

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__WCS417:GFF2243
          Length = 634

 Score =  245 bits (626), Expect = 4e-69
 Identities = 179/581 (30%), Positives = 293/581 (50%), Gaps = 50/581 (8%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDE--HVGFGFRRLSIIDV 58
           MCG++GVF K P A   +   +     + I HRGPDS   + D      FG+ RL ++ +
Sbjct: 1   MCGYIGVFAKQPRAFNPN---MFDAALRAIHHRGPDSSSQWFDPKGQAAFGYVRLGLVGL 57

Query: 59  ENGGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAA 118
            NG QP+  ++    ++ NGE Y+Y  +R ELE  G  F T SD+E+ +  YR +     
Sbjct: 58  GNGTQPIVADEGDLVMMVNGEFYDYQRIRTELEGYGCRFKTSSDSEIAMHLYRRHGVRGL 117

Query: 119 SKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIEIDK 178
            +LRG F  LI+++    L+  RD  G+KPLYYT      YFASE K+L+ A    + D 
Sbjct: 118 KQLRGEFTILIFDRLRKKLFAVRDRVGVKPLYYTEHEGAWYFASEIKALLAAGVPAQWDH 177

Query: 179 EALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPV----QTEE 234
           EA   Y +  F+    T+  +++ V+PG  + I  +  +  + Y+  +F       Q  E
Sbjct: 178 EA---YANRGFILRDRTVFNNIRSVKPGC-WIIADESGLQTEQYWDWDFPDAEATEQRSE 233

Query: 235 DKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEF-HPSLKTFSVGFE-Q 292
            ++++ +R+ I +SV + + +DVPVG  LSGG+DSS ++ +A E    SL+ F + FE +
Sbjct: 234 AEMIESLRNTIEESVRLRLHADVPVGVCLSGGLDSSAMLGIATELTGQSLQAFHLSFEGE 293

Query: 293 QGFSEVDVAKETA----AALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFV 348
           Q + E   A+  A    A L + +++     + + N L    WH + P A+  ++  Y +
Sbjct: 294 QAYDERQYAEVAARHNRAHLNVLSVNSSDMADNFENAL----WHAEMPFANAHSVAKYLL 349

Query: 349 AKEAKKH-VTVALSGEGADELFGGYNIYREPLSLKPFE-RIPSGLKKM--LLHVA--AVM 402
            K  +   +   L+GEGADE+FGGY  YR  + L   E + PS + ++   LH +    +
Sbjct: 350 CKYVQNQGMRAVLTGEGADEVFGGYPHYRRDMVLYNHENQDPSAIAELSRRLHASEDRYL 409

Query: 403 PEGMRG----KSLLERGCTPLQDR---YIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTY 455
           P G       +  L  G + LQ +   +   A+++ +         ++   S+ D  + +
Sbjct: 410 PGGKNDVKWVQDELGHGVSWLQTQSALFGPLAQLYSDD--------FHERFSHTDAYREF 461

Query: 456 FTESS-----SYSDINKMQYVDIHTWMRGDILLK-ADKMTMANSLELRVPFLDKVVFDVA 509
           +   S      +  +N+  Y+   + +   +L    D+M MA SLE R P LD  V + A
Sbjct: 462 YDRLSPRALNGWEPVNRSLYMVAKSSLPNVVLTSLGDRMEMAGSLEGRPPLLDHQVIEAA 521

Query: 510 SKIPDELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVP 550
            ++P  +K +  T KY LR+A    VP+ VL+RKK  F  P
Sbjct: 522 CRLPVNMKVRGATEKYALREAMRPYVPQAVLDRKKQYFRAP 562


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: 887
Number of extensions: 43
Number of successful extensions: 7
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: 634
Length adjustment: 38
Effective length of query: 594
Effective length of database: 596
Effective search space:   354024
Effective search space used:   354024
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 GFF2243 PS417_11435 (asparagine synthase)
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.31168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.6e-129  419.1   0.0   1.9e-129  418.9   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF2243  PS417_11435 asparagine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2243  PS417_11435 asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.9   0.0  1.9e-129  1.9e-129       1     517 []       2     559 ..       2     559 .. 0.90

  Alignments for each domain:
  == domain 1  score: 418.9 bits;  conditional E-value: 1.9e-129
                           TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evviv 74 
                                         Cg +g+++++  a +  +  ++ l++++hRGPD++  w d ++ +a++g +RL  + l +g+QP+ +++   v++
  lcl|FitnessBrowser__WCS417:GFF2243   2 CGYIGVFAKQPRAFN-PNMFDAALRAIHHRGPDSSSQWFD-PKGQAAFGYVRLGLVGLGNGTQPIVADEgDLVMM 74 
                                         9999*9999887666.468888899***************.9***********************9999999*** PP

                           TIGR01536  75 fnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLY 149
                                         +nGE Y ++ +r ele  G +F+t sD+E+ +++y+ +g + +++L+G+F + ++d+ +++lf++RDr+G+kPLY
  lcl|FitnessBrowser__WCS417:GFF2243  75 VNGEFYDYQRIRTELEGYGCRFKTSSDSEIAMHLYRRHGVRGLKQLRGEFTILIFDRLRKKLFAVRDRVGVKPLY 149
                                         *************************************************************************** PP

                           TIGR01536 150 yaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekleeywev 221
                                         y++++g+ +faSEiKalla+  ++a+ d+ea+a+   +    +++t+f++++ ++p+      ++  + e+yw+ 
  lcl|FitnessBrowser__WCS417:GFF2243 150 YTEHEGAWYFASEIKALLAAG-VPAQWDHEAYANRGFIL---RDRTVFNNIRSVKPGCWIiadESGLQTEQYWDW 220
                                         ********************9.99****99999887766...49************998888667777888**99 PP

                           TIGR01536 222 ekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfedskd 292
                                         + +      + se e++e+lr+++e++v+ rl+advpvgv+lSGGlDSs++  ia +   ++++ F + fe++++
  lcl|FitnessBrowser__WCS417:GFF2243 221 DFPDaeatEQRSEAEMIESLRNTIEESVRLRLHADVPVGVCLSGGLDSSAMLGIATELTGQSLQAFHLSFEGEQA 295
                                         98887788888999************************************************************* PP

                           TIGR01536 293 ldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDEl 367
                                         +de ++a+ +a++ + +++ + +++ ++++++e+ +++ e p+a++ s+  yll+k+++++g++ vL+GeGaDE+
  lcl|FitnessBrowser__WCS417:GFF2243 296 YDERQYAEVAARHNRAHLNVLSVNSSDMADNFENALWHAEMPFANAHSVAKYLLCKYVQNQGMRAVLTGEGADEV 370
                                         *************************************************************************** PP

                           TIGR01536 368 fgGYeyfreakaeeale................lpeaselaekkl.......................llqakla 403
                                         fgGY  +r+  +  + e                           +                        lq++ a
  lcl|FitnessBrowser__WCS417:GFF2243 371 FGGYPHYRRDMVLYNHEnqdpsaiaelsrrlhaS----------EdrylpggkndvkwvqdelghgvsWLQTQSA 435
                                         ********98877777666777744433333330..........1445666666666667777777775555556 PP

                           TIGR01536 404 keselkellkakleeelkekeelkkelkee........seleellrldlelllsdllrak..DrvsmahslEvRv 468
                                             l++l + +++e  +++++  + + +         + +++ l+  ++  l+++++ +  Dr+ ma slE R 
  lcl|FitnessBrowser__WCS417:GFF2243 436 LFGPLAQLYSDDFHERFSHTDAYREFYDRLspralngwEPVNRSLYMVAKSSLPNVVLTSlgDRMEMAGSLEGRP 510
                                         6667777777777777777777777666668888999999****************999999************* PP

                           TIGR01536 469 PflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                         P+lD++++e+a ++p+++k+r  +eK+ Lrea++ ++P+++l+RkK+ f
  lcl|FitnessBrowser__WCS417:GFF2243 511 PLLDHQVIEAACRLPVNMKVRGATEKYALREAMRPYVPQAVLDRKKQYF 559
                                         **********************************************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (634 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: 00:00:00.02
# Mc/sec: 12.47
//
[ok]

This GapMind analysis is from Apr 09 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