Alignments for a candidate for asnB in Rhodomicrobium vannielii ATCC 17100

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Rhodomicrobium vannielii ATCC 17100

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_013418103.1 RVAN_RS02055 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000166055.1:WP_013418103.1
          Length = 669

 Score =  344 bits (882), Expect = 8e-99
 Identities = 249/679 (36%), Positives = 332/679 (48%), Gaps = 70/679 (10%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCGL   ++A      P   D    IAR +  + HRGPD  G W     A  G+  G  R
Sbjct: 1   MCGLTGILSA-----APPSNDVRGTIARMTAALHHRGPDAEGLW-----AEDGIALGHRR 50

Query: 61  LSIIDIAHSH-QPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAV-FATDGDGEA 118
           LSI+D++ +  QP+R     A  R+V+ FNGEIYN+L+LR +L     A  +    D E 
Sbjct: 51  LSILDLSEAGAQPMR----SACGRFVIAFNGEIYNHLDLRRDLEAAGVAPDWRGHSDTET 106

Query: 119 ILAGYHHWGT-EVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEK 177
           +LAG  HWG  E L+R  GMFA ALWD   R L  ARD  G KPL+     G     SE 
Sbjct: 107 LLAGIAHWGLDETLRRAAGMFAIALWDRKERRLSLARDRIGEKPLYWGWAGGALVFGSEL 166

Query: 178 KCLLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIR-------- 229
           K L    +  GF  ++  +AL  Y    YVP P ++H GV +LE GC   +         
Sbjct: 167 KALR---QHPGFPRDVCRQALALYLRFAYVPAPRSIHPGVYKLEPGCILTVDDTPPAAPP 223

Query: 230 ADQLAP-------VITRYFVPRFAASPITND---NDQARYDEITAVLEDSVAKHMRADVT 279
            D L P        I RY+    A      +   ++ A    +   L  +V + M ADV 
Sbjct: 224 QDPLRPGDRHGSLSIRRYWSLNEAIEAGGRNRFTDEVAALGALDTALRAAVGRQMLADVP 283

Query: 280 VGAFLSGGIDSTAIAALAIRHNPRLI-TFTTGFEREGFSEIDVAVASAEAIGARHIAKVV 338
           +GAFLSGGIDS+ I AL    + R + TFT GFE   F E   A A A  +G  H   VV
Sbjct: 284 LGAFLSGGIDSSLIVALMQVQSSRPVKTFTVGFENPAFDEAPFAAAVARHLGTDHTELVV 343

Query: 339 SADEFVAALPEIVWYLDEPVADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYR- 397
           + +E    +P++    DEP AD + +P   V R AR  V V LSG+  DELFGGY  Y  
Sbjct: 344 TENEAREVIPQLPDLYDEPFADSSQIPSHLVCRAARAQVTVALSGDAGDELFGGYNRYFW 403

Query: 398 EPLSLRPFDYLPKPLRRSMGKV--SKPLPEGMRGKSLLHRGSLTLEERYYGNARSFSGAQ 455
            P   R  D++P  LRRS+G    + P+P   R  +++ R      ++ +  A     A+
Sbjct: 404 GPRVWRRLDWMPFGLRRSLGHAIAAVPVPVWDRAGAIVSRSVSRPGDKAHRLA-----AR 458

Query: 456 LREV-------------------LPGFRPDWTHTDVTAPVYAESAGWDPVARMQHIDLFT 496
           LREV                   + GF  D     +  P+       DPV RM   D+ T
Sbjct: 459 LREVETQDDLYRSLVSEWPGQRLVRGFSADLGGV-LDDPLLPSVLEDDPVGRMMAQDMRT 517

Query: 497 WLRGDILVKADKITMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIV 556
           +L  DIL K D+  M  SLE RVPFLDPEV ++++RLP   +I     K+ALR+ L   V
Sbjct: 518 YLPDDILCKVDRAAMGVSLETRVPFLDPEVMSLSARLPPDMRIRDGQGKWALRQILYRHV 577

Query: 557 PAHVLHRPKLGFPVPIRHWLRAGELLEWAYATVGSSQAGH--LVDIAAVYRMLDEHRCGS 614
           P  ++ RPK GF +P+  WLR G L  WA   +         L+D A V +   EH  G 
Sbjct: 578 PRELIERPKTGFGIPVGEWLR-GPLRSWAEDLLSEDALARDDLIDPAPVRQAWAEHLSGR 636

Query: 615 SDHSRRLWTMLIFMLWHAI 633
            D + RLW +L+FM W A+
Sbjct: 637 RDWTYRLWIVLMFMAWRAV 655


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: 1191
Number of extensions: 70
Number of successful extensions: 11
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: 652
Length of database: 669
Length adjustment: 38
Effective length of query: 614
Effective length of database: 631
Effective search space:   387434
Effective search space used:   387434
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_013418103.1 RVAN_RS02055 (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.5745.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-139  452.7   0.0   1.3e-139  452.4   0.0    1.1  1  lcl|NCBI__GCF_000166055.1:WP_013418103.1  RVAN_RS02055 asparagine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000166055.1:WP_013418103.1  RVAN_RS02055 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.4   0.0  1.3e-139  1.3e-139       1     517 []       2     589 ..       2     589 .. 0.88

  Alignments for each domain:
  == domain 1  score: 452.4 bits;  conditional E-value: 1.3e-139
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                               Cg++gi+ +   +++ + +i++m+ +l+hRGPDaeg+w +   ++ +lghrRL+i dlse+ aQP++++
  lcl|NCBI__GCF_000166055.1:WP_013418103.1   2 CGLTGILSAAPPSNDVRGTIARMTAALHHRGPDAEGLWAE---DGIALGHRRLSILDLSEAgAQPMRSA 67 
                                               *********99999988***********************...8***************999******* PP

                                 TIGR01536  69 k.evvivfnGEIYNheeLreeleekGy..eFetksDtEViLaayeewg.eelverLeGmFAfalwdekk 133
                                                 + vi fnGEIYNh +Lr++le++G   +++++sDtE +La + +wg  e++ r +GmFA+alwd+k+
  lcl|NCBI__GCF_000166055.1:WP_013418103.1  68 CgRFVIAFNGEIYNHLDLRRDLEAAGVapDWRGHSDTETLLAGIAHWGlDETLRRAAGMFAIALWDRKE 136
                                               99************************8557*************************************** PP

                                 TIGR01536 134 gelflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevke 202
                                               ++l laRDr+G kPLY +  +g+l+f+SE+Kal +++ +++ + ++ala +l + +vp +++++ +v++
  lcl|NCBI__GCF_000166055.1:WP_013418103.1 137 RRLSLARDRIGEKPLYWGWAGGALVFGSELKALRQHPGFPRDVCRQALALYLRFAYVPAPRSIHPGVYK 205
                                               ********************************************************************* PP

                                 TIGR01536 203 lepakal....................dgeekleeywevekee......vkeseeelveelrelledav 245
                                               lep+  l                    +g+ ++++yw++++        + ++e ++   l+ +l++av
  lcl|NCBI__GCF_000166055.1:WP_013418103.1 206 LEPGCILtvddtppaappqdplrpgdrHGSLSIRRYWSLNEAIeaggrnRFTDEVAALGALDTALRAAV 274
                                               ****999999************9998888889999***99887788776555666777889******** PP

                                 TIGR01536 246 kkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevl 314
                                                +++ advp+g++lSGG+DSsl++a+++ ++ ++vktF++gfe ++++de+ +a++va++lgt+h+e++
  lcl|NCBI__GCF_000166055.1:WP_013418103.1 275 GRQMLADVPLGAFLSGGIDSSLIVALMQVQSSRPVKTFTVGFE-NPAFDEAPFAAAVARHLGTDHTELV 342
                                               *******************************************.************************* PP

                                 TIGR01536 315 iseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeal 383
                                               ++e+e+ + ++++    +ep+a++++ip+ l++++ar++ v+V+LsG+ +DElfgGY++++  ++   +
  lcl|NCBI__GCF_000166055.1:WP_013418103.1 343 VTENEAREVIPQLPDLYDEPFADSSQIPSHLVCRAARAQ-VTVALSGDAGDELFGGYNRYFWGPRV--W 408
                                               ***************************************.******************99875443..3 PP

                                 TIGR01536 384 e..............................................lpeaselaekklllqaklakes 406
                                               +                                               ++  +  e++  l+++l +e+
  lcl|NCBI__GCF_000166055.1:WP_013418103.1 409 RrldwmpfglrrslghaiaavpvpvwdragaivsrsvsrpgdkahrlAAR-LREVETQDDLYRSLVSEW 476
                                               33358888888887777777776666666666544444444443332111.112222224445555666 PP

                                 TIGR01536 407 elkellkakleeelkekeelkkelkee...............seleellrldlelllsdllrak.Drvs 459
                                                 ++l++  ++++                               + +++ +d+ ++l+d+++ k Dr++
  lcl|NCBI__GCF_000166055.1:WP_013418103.1 477 PGQRLVRG-FSAD-------------LggvlddpllpsvledDPVGRMMAQDMRTYLPDDILCKvDRAA 531
                                               66666553.3333.............033344444444445599************************* PP

                                 TIGR01536 460 mahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                               m  slE RvPflD e+++l +++pp++++rdg+ K+ Lr+++ +++P+e+ eR+K +f
  lcl|NCBI__GCF_000166055.1:WP_013418103.1 532 MGVSLETRVPFLDPEVMSLSARLPPDMRIRDGQGKWALRQILYRHVPRELIERPKTGF 589
                                               ********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (669 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: 00:00:00.03
# Mc/sec: 9.57
//
[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