GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asnB in Maridesulfovibrio bastinii DSM 16055

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_027178967.1 G496_RS0108840 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000429985.1:WP_027178967.1
          Length = 651

 Score =  323 bits (829), Expect = 1e-92
 Identities = 206/654 (31%), Positives = 343/654 (52%), Gaps = 54/654 (8%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQ---MNQMIVHRGPDSDGYFHDEHVGFGF--RRLSI 55
           MCG  G  +   L ++ D EEL ++   M +    RGPD+D  + D+ +G  F  RRL+I
Sbjct: 1   MCGISGFID---LTRSLDSEELSRRAGLMGKSQQSRGPDADAQWVDQEIGIAFDHRRLAI 57

Query: 56  IDV-ENGGQPLSYEDETYWIIFNGEIYNYIELREELEAK-GYT-FNTDSDTEVLLATYRH 112
           ID+ E G QP+      Y  +FNGEIYNY ELR ELE   G+  +   SDTEVLL     
Sbjct: 58  IDLTEEGIQPMHSRSGRYVTVFNGEIYNYAELRSELETTAGFNGWRGHSDTEVLLEAIEQ 117

Query: 113 YK-EEAASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQ 171
           +  E++  +  GMFA  +W++ +  L+  RD  G KPL+Y    D  YFASE K++   +
Sbjct: 118 WGLEKSLERFSGMFAIALWDRRERQLFLVRDRMGEKPLFYGRQGDTFYFASELKAIRQLE 177

Query: 172 N-DIEIDKEALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPV 230
           +   EI+++AL  Y+ + +VP P T+   V  + PG+   +  DG ++    + +     
Sbjct: 178 SFKPEINRDALCSYLRYHYVPSPGTIYNKVSSLMPGTWIRVDYDGTVSGPFSYWSLKDCA 237

Query: 231 QTEED--------KLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPS 282
           Q   D        ++   + D +   +   M SDVP+G+FLSGG+DSS IV++ ++   +
Sbjct: 238 QKGVDLSFTASSGEITDTLEDLLLKVIEREMVSDVPLGAFLSGGVDSSLIVALMQQCALA 297

Query: 283 -LKTFSVGFEQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPA 341
            +KTF++GF+ + ++E + A + AA +G E+    ++P + ++ +PKI   +D P +D +
Sbjct: 298 PVKTFTIGFDDKAYNEAEEAAKVAAYIGTEHTELYVTPADALDVIPKIPKIWDQPFSDAS 357

Query: 342 AIPLYFVAKEAKKHVTVALSGEGADELFGGYNIYREPLSL-KPFERIPSGLKKMLLH--- 397
            +P + V+   +KHVTVALSG+G DELF GYN + +   L      +P G++K       
Sbjct: 358 QVPTHLVSMMTRKHVTVALSGDGGDELFAGYNRHFKGCGLWDKLASVPPGIRKFTAESLQ 417

Query: 398 -------------VAAVMPEGMR----GKSLLERG----CTPLQDRYIGNAKIFEESVKK 436
                        +  V+P  ++    G+ L +          +D Y+     + +  K 
Sbjct: 418 KVPANEWNAFFEIIDPVLPRKLKMRLPGQKLHKLADVMTAASARDYYLKLTSNWFDPEKL 477

Query: 437 QLLKHYNPNLSYRDVTKTYFTESSSYSDINKMQYVDIHTWMRGDILLKADKMTMANSLEL 496
            +    +P      V +    E+S  ++   MQ++D  T++  DI+ K D+  MA SLE 
Sbjct: 478 VINGWEHPGPYQSPVNQ---PETSCLTE--WMQFMDAATYLPDDIMTKVDRAAMAVSLET 532

Query: 497 RVPFLDKVVFDVASKIPDELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLK 556
           R PFLD  + + + ++P  LK ++G  K +LR      VP+ ++ R K+GF +PI  WL+
Sbjct: 533 RAPFLDHEIVEFSQRLPMSLKIQHGRGKKILRDILYKYVPQRLIERPKMGFGIPIDSWLR 592

Query: 557 NEMNEWVRNIIQ--ESQTDAYIHKDYVLQLLEDHCADKADNSRKIWTVLIFMIW 608
             + +WV +++       + Y+H + + ++  DH + K D   KIW +L+F  W
Sbjct: 593 GPLRDWVEDLLNPVRMMNEGYLHPEPIRKMWADHLSGKTDAQYKIWNILVFQSW 646


Lambda     K      H
   0.319    0.136    0.403 

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: 1038
Number of extensions: 57
Number of successful extensions: 8
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: 632
Length of database: 651
Length adjustment: 38
Effective length of query: 594
Effective length of database: 613
Effective search space:   364122
Effective search space used:   364122
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_027178967.1 G496_RS0108840 (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.3821051.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.8e-142  460.4   0.0   7.9e-142  459.7   0.0    1.3  1  NCBI__GCF_000429985.1:WP_027178967.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000429985.1:WP_027178967.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.7   0.0  7.9e-142  7.9e-142       1     517 []       2     583 ..       2     583 .. 0.85

  Alignments for each domain:
  == domain 1  score: 459.7 bits;  conditional E-value: 7.9e-142
                             TIGR01536   1 Cgiagivdlkakake..eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek. 69 
                                           Cgi g++dl++ +++   ++ +  m + ++ RGPDa++ w d +e + ++ hrRLaiidl e   QP+++++ 
  NCBI__GCF_000429985.1:WP_027178967.1   2 CGISGFIDLTRSLDSeeLSRRAGLMGKSQQSRGPDADAQWVD-QEIGIAFDHRRLAIIDLTEEgIQPMHSRSg 73 
                                           ***********9999754567778889999************.799**************8877********* PP

                             TIGR01536  70 evvivfnGEIYNheeLreelee.kGye.FetksDtEViLaayeewg.eelverLeGmFAfalwdekkgelfla 139
                                           ++v vfnGEIYN+ eLr ele+ +G++ ++++sDtEV+L+a+e+wg e+ +er+ GmFA+alwd+++++lfl+
  NCBI__GCF_000429985.1:WP_027178967.1  74 RYVTVFNGEIYNYAELRSELETtAGFNgWRGHSDTEVLLEAIEQWGlEKSLERFSGMFAIALWDRRERQLFLV 146
                                           ********************96268765899****************************************** PP

                             TIGR01536 140 RDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal..d 210
                                           RDr+G kPL+y++++++++faSE+Ka+ +l+++k+e++++al ++l +++vp++ t++++v  l+p+     d
  NCBI__GCF_000429985.1:WP_027178967.1 147 RDRMGEKPLFYGRQGDTFYFASELKAIRQLESFKPEINRDALCSYLRYHYVPSPGTIYNKVSSLMPGTWIrvD 219
                                           ********************************************************************99775 PP

                             TIGR01536 211 geeklee...ywevekee.......vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiak 273
                                            + +++    yw++++ +       +++s  e +++l++ll + +++ +v+dvp+g++lSGG+DSsl++a+++
  NCBI__GCF_000429985.1:WP_027178967.1 220 YDGTVSGpfsYWSLKDCAqkgvdlsFTASSGEITDTLEDLLLKVIEREMVSDVPLGAFLSGGVDSSLIVALMQ 292
                                           5555555788****9988899999999999******************************************* PP

                             TIGR01536 274 keaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyll 346
                                           + a ++vktF+igf+ +k+++e++ a+kva+++gteh+e++++++++l+ ++++  ++++p+++++++p+ l+
  NCBI__GCF_000429985.1:WP_027178967.1 293 QCALAPVKTFTIGFD-DKAYNEAEEAAKVAAYIGTEHTELYVTPADALDVIPKIPKIWDQPFSDASQVPTHLV 364
                                           ***************.9******************************************************** PP

                             TIGR01536 347 sklarekgvkVvLsGeGaDElfgGYeyfrea..kaeeale......................lpeaselaekk 395
                                           s ++r++ v+V+LsG+G+DElf+GY+++++    +++ +                                  
  NCBI__GCF_000429985.1:WP_027178967.1 365 SMMTRKH-VTVALSGDGGDELFAGYNRHFKGcgLWDKLASvppgirkftaeslqkvpanewnA---------- 426
                                           *******.*******************998522455555566666666555555554444440.......... PP

                             TIGR01536 396 l..................................llqaklakeselkellkakleeelkekeelkkelkee. 433
                                           +                                   ++ kl++++                            
  NCBI__GCF_000429985.1:WP_027178967.1 427 FfeiidpvlprklkmrlpgqklhkladvmtaasarDYYLKLTSNW--------------------------Fd 473
                                           055555533333333333333343333222222221222222222..........................02 PP

                             TIGR01536 434 .........................seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelal 480
                                                                      +e ++  d++++l+d++  k Dr++ma slE R+PflD+e+ve+  
  NCBI__GCF_000429985.1:WP_027178967.1 474 peklvingwehpgpyqspvnqpetsCLTEWMQFMDAATYLPDDIMTKvDRAAMAVSLETRAPFLDHEIVEFSQ 546
                                           222223333333444455556665477788999**************************************** PP

                             TIGR01536 481 sippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           ++p++lk+++g+ K +Lr ++ +++P+++ eR+K++f
  NCBI__GCF_000429985.1:WP_027178967.1 547 RLPMSLKIQHGRGKKILRDILYKYVPQRLIERPKMGF 583
                                           ***********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (651 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 12.17
//
[ok]

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

Links

Downloads

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:

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:

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:

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:

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