Alignments for a candidate for asnB in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Methylobacterium nodulans ORS 2060

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_012631017.1 MNOD_RS38500 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000022085.1:WP_012631017.1
          Length = 654

 Score =  210 bits (534), Expect = 2e-58
 Identities = 200/631 (31%), Positives = 280/631 (44%), Gaps = 71/631 (11%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG LA         GP    A S I      +RHRGPDE   W   +    GV  G  R
Sbjct: 1   MCGFLAVFHG-----GPRPL-APSTILAGLSAIRHRGPDERDIWLDPEA---GVALGHTR 51

Query: 61  LSIIDIAHSHQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAIL 120
           LSII +++  QP+            L+ NGE Y++  +R EL+ + G VF T  D E  L
Sbjct: 52  LSIIGLSNGRQPIA----SQDGALQLIVNGEFYDFERIRAELQAR-GCVFRTQSDSEIAL 106

Query: 121 AGYHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKKCL 180
             Y  +GT  L RLRG FA  L+D V R+L   RD FGIKPLF+A   G   V SE K L
Sbjct: 107 HLYREFGTAGLGRLRGEFALVLYDAVERQLVVMRDRFGIKPLFVAEHDGALWVGSEIKAL 166

Query: 181 LDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVITRY 240
           +       +D       L  Y    +     TL +G+R L  G         +      Y
Sbjct: 167 VAAGVPAFWD-------LDAYVSRGFYLGNRTLFQGIRSLAPGHLLIASPGHIRE--RAY 217

Query: 241 FVPRFAASPITNDNDQARYDEITAV------LEDSVAKHMRADVTVGAFLSGGIDSTAIA 294
           +   F A+      D A  DE  AV      + ++V   +RADV +  +LSGGIDS+A+ 
Sbjct: 218 WDLDFPAAAAL---DSAAIDEAEAVEGLRAEILEAVGLRLRADVPIAVYLSGGIDSSAML 274

Query: 295 ALAIR-HNPRLITFTTGFEREG-FSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVW 352
             A R     L  FT  F  +G + E   A  +A   GAR     V+ D+      E +W
Sbjct: 275 GCATRLRGTPLDAFTLSFTDDGDYDERRFAAEAASFNGARFHPIPVTQDDLADDFEEALW 334

Query: 353 YLDEPVADPALVPLFFVAR-EARKHVKVVLSGEGADELFGGYTIYREPLSL----RPFDY 407
           + + P  +   V  + ++R  A+   KVV++GEGADE+F GY  +R  + L    R    
Sbjct: 335 HNEVPFFNAHGVAKYRLSRVVAQARFKVVITGEGADEIFAGYPHFRRDMLLYNAERQDPG 394

Query: 408 LPKPLRRSMGKVSKPLPEGMRGKSLLHRGSLTLEERYYGNARSFSGAQ------LREVLP 461
           L   LR  + +      EG  G + L   +  + +R  G+  S+ G Q      LR +  
Sbjct: 395 LVADLRARLAR-----SEGGYGGTTLPADAAWMTDR-LGHGVSWVGNQSAWFDALRALYD 448

Query: 462 G-----------FRPDWTHTDVTAPVYAESAGWDPVARMQHIDLFTWLRGDILVK-ADKI 509
           G           +R  +   D     +A  AG DP+ R  ++   ++L   +L    D++
Sbjct: 449 GPTRRRSAGIGAYRRFYNGLD-----HARMAGRDPLHRSMYLWAKSFLPNFVLTTLGDRM 503

Query: 510 TMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFP 569
            MANS+E RVP LD  V   A+RLP   KI   T K+  R A+ P +P  +  R K  F 
Sbjct: 504 EMANSIEGRVPLLDHHVAEYAARLPVWLKIRGATEKHVFREAMRPFLPEALYRRKKHYFR 563

Query: 570 VPIRHWLRAGELLEWAYATVGSSQAGHLVDI 600
            P     +   L +    T+ S    HL D+
Sbjct: 564 APPAMSAQRNRLAQLVADTLASR---HLEDL 591


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: 1064
Number of extensions: 59
Number of successful extensions: 7
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: 654
Length adjustment: 38
Effective length of query: 614
Effective length of database: 616
Effective search space:   378224
Effective search space used:   378224
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_012631017.1 MNOD_RS38500 (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.11202.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-125  406.4   0.0   1.8e-125  405.8   0.0    1.3  1  lcl|NCBI__GCF_000022085.1:WP_012631017.1  MNOD_RS38500 asparagine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000022085.1:WP_012631017.1  MNOD_RS38500 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.8   0.0  1.8e-125  1.8e-125       1     517 []       2     562 ..       2     562 .. 0.85

  Alignments for each domain:
  == domain 1  score: 405.8 bits;  conditional E-value: 1.8e-125
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 
                                               Cg++++++       + ++i + l +++hRGPD++ +w d +e++++lgh RL+ii ls+g+QP+++++
  lcl|NCBI__GCF_000022085.1:WP_012631017.1   2 CGFLAVFHGGPRPL-APSTILAGLSAIRHRGPDERDIWLD-PEAGVALGHTRLSIIGLSNGRQPIASQD 68 
                                               66666665544322.33455555789**************.9*************************** PP

                                 TIGR01536  70 .evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137
                                                + ++++nGE Y +e +r+el+++G  F+t+sD+E+ L++y+e+g + + rL+G+FA++l+d+ +++l+
  lcl|NCBI__GCF_000022085.1:WP_012631017.1  69 gALQLIVNGEFYDFERIRAELQARGCVFRTQSDSEIALHLYREFGTAGLGRLRGEFALVLYDAVERQLV 137
                                               *99****************************************************************** PP

                                 TIGR01536 138 laRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkeala.elltlqlvptektlfkevkelep 205
                                               + RDr+GikPL++a+++g+l ++SEiKal+a+  ++a+ d +a++ ++++l     ++tlf++++ l p
  lcl|NCBI__GCF_000022085.1:WP_012631017.1 138 VMRDRFGIKPLFVAEHDGALWVGSEIKALVAAG-VPAFWDLDAYVsRGFYLG----NRTLFQGIRSLAP 201
                                               ********************************9.899999766651566666....68*********** PP

                                 TIGR01536 206 akal..dgeeklee.ywevekee......vkeseeelveelrelledavkkrlvadvpvgvllSGGlDS 265
                                               ++ l  ++ + +e+ yw+++ ++       + +e e+ve lr  + +av  rl+advp++v+lSGG+DS
  lcl|NCBI__GCF_000022085.1:WP_012631017.1 202 GHLLiaSPGHIRERaYWDLDFPAaaaldsAAIDEAEAVEGLRAEILEAVGLRLRADVPIAVYLSGGIDS 270
                                               ****98666666667*****999999998888999********************************** PP

                                 TIGR01536 266 slvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleep 334
                                               s++   a +   +++  F++ f+d+ d+de ++a+++a + g + + + ++++++++++ee +++ e p
  lcl|NCBI__GCF_000022085.1:WP_012631017.1 271 SAMLGCATRLRGTPLDAFTLSFTDDGDYDERRFAAEAASFNGARFHPIPVTQDDLADDFEEALWHNEVP 339
                                               ********************************************************************* PP

                                 TIGR01536 335 tairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale................... 384
                                               + ++  +  y ls+ + +  +kVv++GeGaDE+f+GY  fr+     ++e                   
  lcl|NCBI__GCF_000022085.1:WP_012631017.1 340 FFNAHGVAKYRLSRVVAQARFKVVITGEGADEIFAGYPHFRRDMLLYNAErqdpglvadlrarlarseg 408
                                               *****************************************9988877777789988887777666666 PP

                                 TIGR01536 385 ..........lpeaselaekkl.............llqaklakeselkellkakleeelkekeelkkel 430
                                                                                         ++s+    l+a ++  ++++++  +++
  lcl|NCBI__GCF_000022085.1:WP_012631017.1 409 gyggttlpadA----------AwmtdrlghgvswvG------NQSAWFDALRALYDGPTRRRSAGIGAY 461
                                               66666644443..........033333333333331......222222222222222222222222222 PP

                                 TIGR01536 431 kee............seleellrldlelllsdllrak..DrvsmahslEvRvPflDkelvelalsippe 485
                                                +               l++ ++l ++ +l++ ++    Dr+ ma+s+E RvP+lD++++e+a+++p+ 
  lcl|NCBI__GCF_000022085.1:WP_012631017.1 462 RRFyngldharmagrDPLHRSMYLWAKSFLPNFVLTTlgDRMEMANSIEGRVPLLDHHVAEYAARLPVW 530
                                               222333333444556999**************9999889****************************** PP

                                 TIGR01536 486 lklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                               lk+r  +eK+++rea++  lPe++  RkK+ f
  lcl|NCBI__GCF_000022085.1:WP_012631017.1 531 LKIRGATEKHVFREAMRPFLPEALYRRKKHYF 562
                                               *****************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (654 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 0.01s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 6.00
//
[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