Alignments for a candidate for asnB in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Mycolicibacterium vanbaalenii PYR-1

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_036374485.1 MVAN_RS17900 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000015305.1:WP_036374485.1
          Length = 643

 Score = 1049 bits (2713), Expect = 0.0
 Identities = 519/652 (79%), Positives = 567/652 (86%), Gaps = 9/652 (1%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCGLLA V  P+    P   DA SA   AS  MRHRGPDE GTW+        VV GFNR
Sbjct: 1   MCGLLALVIDPSSEVSPTTVDAVSA---ASAQMRHRGPDEPGTWNDTR-----VVLGFNR 52

Query: 61  LSIIDIAHSHQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAIL 120
           LSIIDIAHSHQPLRWGPPEAP RY LVFNGEIYNYLELRD LR++ GA F TDGDGEAI+
Sbjct: 53  LSIIDIAHSHQPLRWGPPEAPGRYTLVFNGEIYNYLELRDALRSEFGAEFHTDGDGEAIV 112

Query: 121 AGYHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKKCL 180
           A YHHWG + L RLRGMFAFALWD+V +ELFCARDPFGIKPL++ATG GGTAV SEKKCL
Sbjct: 113 AAYHHWGADALTRLRGMFAFALWDSVAQELFCARDPFGIKPLYLATGTGGTAVGSEKKCL 172

Query: 181 LDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVITRY 240
           LD+ + +GFD  +D RA+QHYTVLQYVPEPETLHRG+RRLESG +AR+R     P +TRY
Sbjct: 173 LDIADRLGFDLGVDERAVQHYTVLQYVPEPETLHRGIRRLESGSYARVRPGA-QPEVTRY 231

Query: 241 FVPRFAASPITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDSTAIAALAIRH 300
           F PRF A       +QARYDEITA LEDSVAKHMRADVTVGAFLSGGIDSTAIAALA+RH
Sbjct: 232 FRPRFDAVAFRAGAEQARYDEITAALEDSVAKHMRADVTVGAFLSGGIDSTAIAALAMRH 291

Query: 301 NPRLITFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVWYLDEPVAD 360
           NPRLITFTTGFEREGFSE+DVAVASAEAIGARH+ KVVS  EFVAALPEIVWYLDEPVAD
Sbjct: 292 NPRLITFTTGFEREGFSEVDVAVASAEAIGARHVTKVVSQQEFVAALPEIVWYLDEPVAD 351

Query: 361 PALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYREPLSLRPFDYLPKPLRRSMGKVS 420
           PALVPL+F+AREARKHVKVVLSGEGADELFGGYTIYREPLSL+PFDYLP+ LR+S+G+++
Sbjct: 352 PALVPLYFIAREARKHVKVVLSGEGADELFGGYTIYREPLSLKPFDYLPRGLRKSVGRMA 411

Query: 421 KPLPEGMRGKSLLHRGSLTLEERYYGNARSFSGAQLREVLPGFRPDWTHTDVTAPVYAES 480
            PLPEGMRGKSLLHRGSLTLEERYYGNARSFS AQLR VLP FRP+W HTDVTAPVYA+S
Sbjct: 412 GPLPEGMRGKSLLHRGSLTLEERYYGNARSFSDAQLRAVLPRFRPEWVHTDVTAPVYAQS 471

Query: 481 AGWDPVARMQHIDLFTWLRGDILVKADKITMANSLELRVPFLDPEVFAVASRLPAGAKIT 540
             WDPVARMQHIDLFTWLRGDILVKADK+TMANSLELRVPFLDPEVFAVASRLP   KIT
Sbjct: 472 QDWDPVARMQHIDLFTWLRGDILVKADKMTMANSLELRVPFLDPEVFAVASRLPYDQKIT 531

Query: 541 RTTTKYALRRALEPIVPAHVLHRPKLGFPVPIRHWLRAGELLEWAYATVGSSQAGHLVDI 600
           R+TTKYALRRALEPIVPAHVL+RPKLGFPVPIRHWLR+GELL+WAY  VG+S AG LV++
Sbjct: 532 RSTTKYALRRALEPIVPAHVLNRPKLGFPVPIRHWLRSGELLDWAYGMVGTSGAGDLVEL 591

Query: 601 AAVYRMLDEHRCGSSDHSRRLWTMLIFMLWHAIFVEHSVVPQISEPQYPVQL 652
           AAV  MLDEHR G++DHSRRLWT+LIFMLW+AIFV+ +V PQISEP YPVQL
Sbjct: 592 AAVRAMLDEHRSGTTDHSRRLWTVLIFMLWYAIFVDKTVTPQISEPTYPVQL 643


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: 1432
Number of extensions: 48
Number of successful extensions: 3
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: 643
Length adjustment: 38
Effective length of query: 614
Effective length of database: 605
Effective search space:   371470
Effective search space used:   371470
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_036374485.1 MVAN_RS17900 (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.3795167.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.7e-146  473.0   0.0   8.8e-146  472.8   0.0    1.0  1  NCBI__GCF_000015305.1:WP_036374485.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015305.1:WP_036374485.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.8   0.0  8.8e-146  8.8e-146       1     517 []       2     559 ..       2     559 .. 0.89

  Alignments for each domain:
  == domain 1  score: 472.8 bits;  conditional E-value: 8.8e-146
                             TIGR01536   1 Cgiagivdlkakake..eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.. 69 
                                           Cg++++v +    ++  + +a+++ + +++hRGPD+ g+w+d   ++++lg++RL+iid+ + +QPl+     
  NCBI__GCF_000015305.1:WP_036374485.1   2 CGLLALVIDPSSEVSptTVDAVSAASAQMRHRGPDEPGTWND---TRVVLGFNRLSIIDIAHSHQPLRWGPpe 71 
                                           88888887776666667889999999****************...8*********************986666 PP

                             TIGR01536  70 ...evvivfnGEIYNheeLreeleek.GyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelfl 138
                                              ++++vfnGEIYN+ eLr+ l+ + G eF+t+ D E i+aay++wg +++ rL+GmFAfalwd+ ++elf 
  NCBI__GCF_000015305.1:WP_036374485.1  72 apgRYTLVFNGEIYNYLELRDALRSEfGAEFHTDGDGEAIVAAYHHWGADALTRLRGMFAFALWDSVAQELFC 144
                                           6899*******************8655********************************************** PP

                             TIGR01536 139 aRDrlGikPLYyaseqgkllfaSEiKallalk...eikaeldkealaelltlqlvptektlfkevkelepaka 208
                                           aRD++GikPLY a+ +g  +++SE+K+ll++     ++  +d+ a+++++ lq+vp+++tl++++++le +++
  NCBI__GCF_000015305.1:WP_036374485.1 145 ARDPFGIKPLYLATGTGGTAVGSEKKCLLDIAdrlGFDLGVDERAVQHYTVLQYVPEPETLHRGIRRLESGSY 217
                                           *******************************98888999********************************** PP

                             TIGR01536 209 l....dgeekleeywevekee...vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakk 274
                                           +      + ++ +y++ + ++   ++  e++  +e+  +led+v+k+++adv vg++lSGG+DS+++aa+a +
  NCBI__GCF_000015305.1:WP_036374485.1 218 ArvrpGAQPEVTRYFRPRFDAvafRAGAEQARYDEITAALEDSVAKHMRADVTVGAFLSGGIDSTAIAALAMR 290
                                           9885544445556***999998888889999****************************************** PP

                             TIGR01536 275 eaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplylls 347
                                           + + ++ tF+ gfe  + ++e ++a + a+++g +h + ++s++e++++l+e++++l+ep+a++a +ply+++
  NCBI__GCF_000015305.1:WP_036374485.1 291 HNP-RLITFTTGFE-REGFSEVDVAVASAEAIGARHVTKVVSQQEFVAALPEIVWYLDEPVADPALVPLYFIA 361
                                           *88.8*********.********************************************************** PP

                             TIGR01536 348 klarekgvkVvLsGeGaDElfgGYeyfreakaeeale................lpease..laekkl...... 396
                                           ++ar++ vkVvLsGeGaDElfgGY ++re+ + + +                 lpe ++       l      
  NCBI__GCF_000015305.1:WP_036374485.1 362 REARKH-VKVVLSGEGADELFGGYTIYREPLSLKPFDylprglrksvgrmagpLPEGMRgkS----Llhrgsl 429
                                           ******.******************************9777777777776666444444330....1334445 PP

                             TIGR01536 397 ......llqaklakeselkellkakleeelkekeelkkelkee...seleellrldlelllsdllrak.Drvs 459
                                                   +a+ ++  +l+ +l  +++ e  +++ ++  ++++     ++++++ dl ++l++++++k D+++
  NCBI__GCF_000015305.1:WP_036374485.1 430 tleeryYGNARSFSDAQLRAVL-PRFRPEWVHTDVTAPVYAQSqdwDPVARMQHIDLFTWLRGDILVKaDKMT 501
                                           5444334444444444444433.3555555555555555544457799************************* PP

                             TIGR01536 460 mahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           ma+slE+RvPflD e++ +a ++p + k+ + ++K+ Lr+a+e ++P ++l+R+K +f
  NCBI__GCF_000015305.1:WP_036374485.1 502 MANSLELRVPFLDPEVFAVASRLPYDQKITRSTTKYALRRALEPIVPAHVLNRPKLGF 559
                                           *******************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (643 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 37.36
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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