Alignments for a candidate for asnB in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Dyella japonica UNC79MFTsu3.2

Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate N515DRAFT_1546 N515DRAFT_1546 asparagine synthase (glutamine-hydrolysing)

Query= CharProtDB::CH_002444
         (554 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1546
          Length = 559

 Score =  674 bits (1739), Expect = 0.0
 Identities = 340/560 (60%), Positives = 412/560 (73%), Gaps = 10/560 (1%)

Query: 1   MCSIFGVFDIKT--DAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNA 58
           MCSIFG+FD++   D   LR++ALELS+  RHRGPDWSG++     IL HERL+IVD  +
Sbjct: 1   MCSIFGMFDLQPGDDLAGLRRQALELSQRQRHRGPDWSGVFVDAGVILVHERLAIVDPAS 60

Query: 59  GAQPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEF---- 114
           G+QPL ++++T  LAVNGEIYNH+ LRA  G  Y F TGSDCEVI ALY+E GPE     
Sbjct: 61  GSQPLRSREETLALAVNGEIYNHRELRAASG--YDFTTGSDCEVINALYRELGPEEFLAR 118

Query: 115 -LDDLQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIK 173
            +  L G+FAFAL+DS    YLI RD +G+ PLY G+D  G+L VASEMKALV VC  + 
Sbjct: 119 GIKQLNGIFAFALWDSATQRYLIARDPIGVCPLYWGHDGEGRLCVASEMKALVGVCADVS 178

Query: 174 EFPAGSYLWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVL 233
            FP G    S  GE+  YY + W  Y+       + + LR A E +V   LM+DVPYGVL
Sbjct: 179 AFPPGHVYDSATGEVTRYYRKHWRSYEVTHGQQLEPSALRGAFEQAVHRQLMTDVPYGVL 238

Query: 234 LSGGLDSSIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGT 293
           LSGGLDSS+++A   ++A  R+ED +RSEAWWP+LHSFA+GL GSPDL AAQ  A+ LGT
Sbjct: 239 LSGGLDSSLVAACAARFARERIEDDDRSEAWWPRLHSFAIGLEGSPDLAAAQVAADALGT 298

Query: 294 VHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDE 353
           VHH   +T  EGLDA+ +VI HIETYDVTTIRASTPM+L++R+IKAMG+KMVLSGEGSDE
Sbjct: 299 VHHGFVYTFWEGLDALPEVIRHIETYDVTTIRASTPMFLLARRIKAMGVKMVLSGEGSDE 358

Query: 354 VFGGYLYFHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVA 413
           +FGGYLYFHKAP+ +  HEETVRKL ALH +DC RANKAM AWGVEARVPFLD +FLDVA
Sbjct: 359 IFGGYLYFHKAPSPEAFHEETVRKLDALHSFDCLRANKAMMAWGVEARVPFLDLEFLDVA 418

Query: 414 MRINPQDKMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQV 473
           M ++ + KM G+G++EK +LRE F+  LP S+ WRQKEQFSDGVGY WID LK  A Q V
Sbjct: 419 MGLDARYKMAGHGRIEKAVLREAFQGALPDSILWRQKEQFSDGVGYGWIDGLKAHAEQVV 478

Query: 474 SDQQLETARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDE 533
           SD++   A  RFP+N P +KEAYLYR IFE+ FP  + A  VPGG S+ACSS  A+ WD 
Sbjct: 479 SDREFAAASTRFPHNPPATKEAYLYRRIFEQHFPGEACAATVPGGKSIACSSPAALAWDP 538

Query: 534 AFKKMDDPSGRAV-GVHQSA 552
           AF    DPSGRAV GVHQ A
Sbjct: 539 AFAAAADPSGRAVRGVHQQA 558


Lambda     K      H
   0.319    0.135    0.407 

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: 919
Number of extensions: 24
Number of successful extensions: 4
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: 554
Length of database: 559
Length adjustment: 36
Effective length of query: 518
Effective length of database: 523
Effective search space:   270914
Effective search space used:   270914
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 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate N515DRAFT_1546 N515DRAFT_1546 (asparagine synthase (glutamine-hydrolysing))
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.32461.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.3e-134  434.6   0.0     4e-111  358.4   0.0    2.6  2  lcl|FitnessBrowser__Dyella79:N515DRAFT_1546  N515DRAFT_1546 asparagine syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_1546  N515DRAFT_1546 asparagine synthase (glutamine-hydrolysing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.4   0.0    4e-111    4e-111       1     386 [.       2     378 ..       2     387 .. 0.94
   2 !   74.4   0.0   4.8e-25   4.8e-25     438     517 .]     378     458 ..     376     458 .. 0.92

  Alignments for each domain:
  == domain 1  score: 358.4 bits;  conditional E-value: 4e-111
                                    TIGR01536   1 Cgiagivdlkakake..eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQP 64 
                                                  C+i+g++dl+   +    ++++ e++++++hRGPD++gv+ d   +++il+h+RLai+d  +g QP
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1546   2 CSIFGMFDLQPGDDLagLRRQALELSQRQRHRGPDWSGVFVD---AGVILVHERLAIVDPASGSQP 64 
                                                  *********87655567789999*******************...7******************** PP

                                    TIGR01536  65 lsnek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewg.eelv....erLeGmF 124
                                                  l++++ + ++ +nGEIYNh+eLr    + Gy+F+t sD+EVi a+y+e+g ee++    ++L+G F
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1546  65 LRSREeTLALAVNGEIYNHRELR---AASGYDFTTGSDCEVINALYRELGpEEFLargiKQLNGIF 127
                                                  ****999****************...789********************988875222268***** PP

                                    TIGR01536 125 AfalwdekkgelflaRDrlGikPLYyase.qgkllfaSEiKallalk.eikaeldkealaelltlq 188
                                                  Afalwd++++++++aRD++G++PLY + + +g+l++aSE+Kal+ ++ ++ a+++++++ + ++++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1546 128 AFALWDSATQRYLIARDPIGVCPLYWGHDgEGRLCVASEMKALVGVCaDVSAFPPGHVYDSATGEV 193
                                                  *****************************99*********************************** PP

                                    TIGR01536 189 lvptektlfkevkelepakaldgeekleeywevekeevkeseeelveelrelledavkkrlvadvp 254
                                                  +    ++++k+++ +e  + +    +le                  + lr ++e+av+++l++dvp
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1546 194 T----RYYRKHWRSYEVTHGQ----QLEP-----------------SALRGAFEQAVHRQLMTDVP 234
                                                  5....79******99988886....4443.................469***************** PP

                                    TIGR01536 255 vgvllSGGlDSslvaaiakkeak.............sevktFsigfedskdldeskaarkvadelg 307
                                                  +gvllSGGlDSslvaa a+++a+              ++++F+ig+e+s+dl    aa+ +ad+lg
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1546 235 YGVLLSGGLDSSLVAACAARFAReriedddrseawwPRLHSFAIGLEGSPDLA---AAQVAADALG 297
                                                  **********************99************9****************...********** PP

                                    TIGR01536 308 tehkevliseeevlkeleevilale..eptairasiplyllsklarekgvkVvLsGeGaDElfgGY 371
                                                  t h+ ++ +  e+l++l+evi+++e  ++t+iras+p++ll+++++++gvk+vLsGeG+DE+fgGY
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1546 298 TVHHGFVYTFWEGLDALPEVIRHIEtyDVTTIRASTPMFLLARRIKAMGVKMVLSGEGSDEIFGGY 363
                                                  ****************************************************************** PP

                                    TIGR01536 372 eyfreakaeealelp 386
                                                   yf++a++ ea++  
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1546 364 LYFHKAPSPEAFHEE 378
                                                  ***********9943 PP

  == domain 2  score: 74.4 bits;  conditional E-value: 4.8e-25
                                    TIGR01536 438 ellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr..dgkeKvlLreaa 501
                                                  e++r+  +l+  d+lra+ +++ma+++E+RvPflD e++++a+ +++ +k+      eK +Lrea+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1546 378 ETVRKLDALHSFDCLRAN-KAMMAWGVEARVPFLDLEFLDVAMGLDARYKMAghGRIEKAVLREAF 442
                                                  5666666788899*****.********************************987889********* PP

                                    TIGR01536 502 eellPeeileRkKeaf 517
                                                  ++ lP++il+R+Ke+f
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1546 443 QGALPDSILWRQKEQF 458
                                                  **************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (559 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: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 5.36
//
[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