Alignments for a candidate for asnB in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_012408102.1 NPUN_RS06985 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000020025.1:WP_012408102.1
          Length = 649

 Score =  298 bits (762), Expect = 7e-85
 Identities = 218/665 (32%), Positives = 324/665 (48%), Gaps = 56/665 (8%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG+  F       +G E  D    I + S  + HRGPD+ G W  V+    GV  G  R
Sbjct: 1   MCGITGFWDISKQFSG-EHLD--ETIQKMSKTLLHRGPDDGGIWTDVEV---GVALGHRR 54

Query: 61  LSIIDIAH-SHQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAI 119
           LSI+D++   HQP+      A  RY++VFNGEIYN+LELR EL TQ G  F    D E +
Sbjct: 55  LSIVDLSPLGHQPMM----SANGRYMVVFNGEIYNFLELRREL-TQLGHNFRGHSDTEIM 109

Query: 120 LAGYHHWGTE-VLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKK 178
           LAG+  WG +  ++R  GMFAFALWD   R L   RD  G KPL+           SE K
Sbjct: 110 LAGFSEWGLDKAIRRFNGMFAFALWDRQKRILHLGRDRLGEKPLYYGWQGSTFLFTSELK 169

Query: 179 CLLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVIT 238
            L        F  EI+  AL  +    Y+P P ++++G+ +L  G           P   
Sbjct: 170 ALK---AHPNFRAEINRDALTQFFRYSYLPAPYSIYQGIYKLPPGTLLSWNGIDAHPDPV 226

Query: 239 RYFVPRFA-----ASPITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDSTAI 293
            Y+  R       A P      +A   ++ A+L ++V   M ADV +GAF+SGGIDS+ I
Sbjct: 227 TYWSAREVTELGIAEPFMGSESEAVI-QLEALLREAVGLRMVADVPLGAFISGGIDSSTI 285

Query: 294 AALAIRHNPRLI-TFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVW 352
            AL    + + + TFT GF  E ++E   A A A+ +G  H    V+  E +  +P++ +
Sbjct: 286 VALMQAQSSQPVKTFTIGFNEEAYNEAKHAKAVAKHLGTDHTELYVNPKEALEVIPKLPF 345

Query: 353 YLDEPVADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYREPLSL-RPFDYLPKP 411
             DEP +D + +P F V++ A++ V V LSG+G DELF GY  Y     + +   ++P  
Sbjct: 346 LYDEPFSDVSQIPTFLVSQLAKQQVTVSLSGDGGDELFAGYNRYLFGRKIWQAIGWIPTT 405

Query: 412 LRRSMGKVSKPLPEGMRGKSLLHRGSL---TLEERYYGN-ARSFSGAQLREVLPGFRPDW 467
           +R++  +    +      +   +  +L    +++  +GN   +FS     E++    P  
Sbjct: 406 VRKNSARALTSVSPQNWNRGFANVNALLPSRIKQPEFGNKLHTFS-----EIMALPNPTA 460

Query: 468 THTDVTA----------------PVYAESAGW----DPVARMQHIDLFTWLRGDILVKAD 507
            +T + +                 + + S  W    D    M + D  T+L  DILVK D
Sbjct: 461 IYTKLVSHWEDPKALVIDGLEPPTILSNSQNWPHLLDFTQCMMYFDTVTYLPDDILVKVD 520

Query: 508 KITMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLG 567
           + +M  SLE R+PFLD  +   A RLP   KI     K+ LR+ L   VP  ++ RPK+G
Sbjct: 521 RASMGVSLEGRIPFLDHRLVEFAWRLPLSMKIRNGQGKWLLRQVLYKYVPPTLVERPKVG 580

Query: 568 FPVPIRHWLRAGELLEWAYATVGSSQAGH--LVDIAAVYRMLDEHRCGSSDHSRRLWTML 625
           F VPI  WLR G L +WA   +  ++  +    +   +    +EH  G++    RLW +L
Sbjct: 581 FGVPINSWLR-GPLRDWAEELLNENRLKNEGFFNPKPIREKWEEHLSGAASWEYRLWDVL 639

Query: 626 IFMLW 630
           +F  W
Sbjct: 640 MFQAW 644


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: 1079
Number of extensions: 59
Number of successful extensions: 9
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: 652
Length of database: 649
Length adjustment: 38
Effective length of query: 614
Effective length of database: 611
Effective search space:   375154
Effective search space used:   375154
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_012408102.1 NPUN_RS06985 (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.1908838.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.4e-158  512.5   0.0   1.1e-157  512.0   0.0    1.2  1  NCBI__GCF_000020025.1:WP_012408102.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020025.1:WP_012408102.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  512.0   0.0  1.1e-157  1.1e-157       1     517 []       2     581 ..       2     581 .. 0.88

  Alignments for each domain:
  == domain 1  score: 512.0 bits;  conditional E-value: 1.1e-157
                             TIGR01536   1 Cgiagivdlkakake..eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek. 69 
                                           Cgi+g+ d +++ +     e+i++m++tl hRGPD+ g+w d  e +++lghrRL+i+dls   +QP+ +++ 
  NCBI__GCF_000020025.1:WP_012408102.1   2 CGITGFWDISKQFSGehLDETIQKMSKTLLHRGPDDGGIWTD-VEVGVALGHRRLSIVDLSPLgHQPMMSANg 73 
                                           *********999887776699*********************.699***************999****99999 PP

                             TIGR01536  70 evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewg.eelverLeGmFAfalwdekkgelflaRD 141
                                           ++++vfnGEIYN+ eLr+el + G++F+++sDtE++La + ewg  +++ r++GmFAfalwd++k+ l+l RD
  NCBI__GCF_000020025.1:WP_012408102.1  74 RYMVVFNGEIYNFLELRRELTQLGHNFRGHSDTEIMLAGFSEWGlDKAIRRFNGMFAFALWDRQKRILHLGRD 146
                                           ************************************************************************* PP

                             TIGR01536 142 rlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal..... 209
                                           rlG kPLYy+ +++++lf SE+Kal a+++++ae++++al++++ +++ p + ++++++++l+p+  l     
  NCBI__GCF_000020025.1:WP_012408102.1 147 RLGEKPLYYGWQGSTFLFTSELKALKAHPNFRAEINRDALTQFFRYSYLPAPYSIYQGIYKLPPGTLLswngi 219
                                           ***********************************************99*******************87555 PP

                             TIGR01536 210 dgeekleeywevekee.......vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakke 275
                                           d + +  +yw++++ +       +  se+e+v +l+ ll++av  r+vadvp+g+++SGG+DSs+++a+++++
  NCBI__GCF_000020025.1:WP_012408102.1 220 DAHPDPVTYWSAREVTelgiaepFMGSESEAVIQLEALLREAVGLRMVADVPLGAFISGGIDSSTIVALMQAQ 292
                                           44444444**99988889*99999999********************************************** PP

                             TIGR01536 276 aksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsk 348
                                           + ++vktF+igf+ +++++e+k+a++va++lgt+h+e++++++e+l+ ++++ +  +ep+++ ++ip++l+s+
  NCBI__GCF_000020025.1:WP_012408102.1 293 SSQPVKTFTIGFN-EEAYNEAKHAKAVAKHLGTDHTELYVNPKEALEVIPKLPFLYDEPFSDVSQIPTFLVSQ 364
                                           *************.9********************************************************** PP

                             TIGR01536 349 larekgvkVvLsGeGaDElfgGYeyfreakaeeale................................lpeas 389
                                           la+++ v+V LsG+G+DElf+GY+++     ++ ++                                     
  NCBI__GCF_000020025.1:WP_012408102.1 365 LAKQQ-VTVSLSGDGGDELFAGYNRYLFG--RKIWQaigwipttvrknsaraltsvspqnwnrgfanvN---- 430
                                           *****.********************985..55555556866666666666665555555555544440.... PP

                             TIGR01536 390 elaekkl............................llqaklakeselkellkakleeelkekeelkkelkee. 433
                                                                              ++++kl +++e+ + l     ++l+  + l+++ ++  
  NCBI__GCF_000020025.1:WP_012408102.1 431 ------AllpsrikqpefgnklhtfseimalpnptAIYTKLVSHWEDPKALVI---DGLEPPTILSNSQNWPh 494
                                           ......04444444555555566666666666666555555555555554443...44444444444444445 PP

                             TIGR01536 434 ..seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaee 503
                                               ++ +++ d+ ++l+d++++k Dr+sm  slE R+PflD++lve+a+++p ++k+r+g+ K+lLr+++ +
  NCBI__GCF_000020025.1:WP_012408102.1 495 llDFTQCMMYFDTVTYLPDDILVKvDRASMGVSLEGRIPFLDHRLVEFAWRLPLSMKIRNGQGKWLLRQVLYK 567
                                           55778899***************************************************************** PP

                             TIGR01536 504 llPeeileRkKeaf 517
                                           ++P  ++eR+K +f
  NCBI__GCF_000020025.1:WP_012408102.1 568 YVPPTLVERPKVGF 581
                                           ***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (649 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: 00:00:00.01
# Mc/sec: 17.84
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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