Aligments for a candidate for asnB in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Aligments for a candidate for asnB in Bacteroides thetaiotaomicron VPI-5482

Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate 350079 BT0551 asparagine synthetase B [glutamine-hydrolyzing] (NCBI ptt file)

Query= CharProtDB::CH_002444
         (554 letters)



>FitnessBrowser__Btheta:350079
          Length = 559

 Score =  758 bits (1957), Expect = 0.0
 Identities = 362/554 (65%), Positives = 445/554 (80%), Gaps = 1/554 (0%)

Query: 1   MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60
           MC I G+ +IKT   ELR KAL++++ +RHRGPDWSGIY   +AILAHERLSIVD  +G 
Sbjct: 1   MCGIAGILNIKTQTKELRDKALKMAQKIRHRGPDWSGIYVGGSAILAHERLSIVDPQSGG 60

Query: 61  QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120
           QPLY+  +   LAVNGEIYNH+ +RA Y  +Y FQTGSDCEVILALY++KG  FL+++ G
Sbjct: 61  QPLYSPDRKQALAVNGEIYNHRDIRARYAGQYDFQTGSDCEVILALYKDKGIHFLEEISG 120

Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180
           +FAF LYD EKD +LI RD +G+IPLY+G D+ G++Y  SE+KAL   C   + F  G Y
Sbjct: 121 IFAFVLYDEEKDEFLIARDPIGVIPLYIGKDKDGKIYFGSELKALEGFCNEYEPFLPGHY 180

Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240
            +S++G+++ +Y R+W DY++VKDN    +++++ALED+V   LMSDVPYGVLLSGGLDS
Sbjct: 181 FYSKEGKMKRWYTREWTDYESVKDNDAKVSDVKEALEDAVHRQLMSDVPYGVLLSGGLDS 240

Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300
           S+ISAI KKYAA+R+E    S+AWWPQLHSFA+GL G+PDL  A+EVA ++GTVHHEI++
Sbjct: 241 SVISAIAKKYAAKRIETDGASDAWWPQLHSFAIGLKGAPDLIKAREVAEYIGTVHHEINY 300

Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360
           TVQEGLDAIRDVIY IETYDVTT+RASTPMYL++R IK+MGIKMVLSGEG+DEVFGGYLY
Sbjct: 301 TVQEGLDAIRDVIYFIETYDVTTVRASTPMYLLARVIKSMGIKMVLSGEGADEVFGGYLY 360

Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420
           FHKAP  K+ HEETVRKL  LHMYDC RANK++SAWGVE RVPFLDK+FLDVAM +NP+ 
Sbjct: 361 FHKAPTPKDFHEETVRKLSKLHMYDCLRANKSLSAWGVEGRVPFLDKEFLDVAMALNPKA 420

Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480
           KMC   ++EK I+RE F   LP SVAWRQKEQFSDGVGYSWIDTL+E+ A  VSD+Q+E 
Sbjct: 421 KMCPGKEIEKRIVREAFADMLPESVAWRQKEQFSDGVGYSWIDTLREITAAAVSDEQMEH 480

Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540
           A  RFP NTP +KE Y YR IFEE FP  SAA  VP  PSVACS+A+A+ WD AF+ +++
Sbjct: 481 AAERFPINTPLNKEEYYYRSIFEEHFPSESAARSVPSVPSVACSTAEALAWDVAFRNLNE 540

Query: 541 PSGRAV-GVHQSAY 553
           PSGRAV GVH+ AY
Sbjct: 541 PSGRAVRGVHEEAY 554


Lambda     K      H
   0.319    0.135    0.407 

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: 935
Number of extensions: 27
Number of successful extensions: 1
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: 554
Length of database: 559
Length adjustment: 36
Effective length of query: 518
Effective length of database: 523
Effective search space:   270914
Effective search space used:   270914
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 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate 350079 BT0551 (asparagine synthetase B [glutamine-hydrolyzing] (NCBI ptt file))
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.12151.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   6.1e-142  460.1   0.1   2.8e-118  382.0   0.0    2.7  2  lcl|FitnessBrowser__Btheta:350079  BT0551 asparagine synthetase B [


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350079  BT0551 asparagine synthetase B [glutamine-hydrolyzing] (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.0   0.0  2.8e-118  2.8e-118       1     384 [.       2     371 ..       2     378 .. 0.97
   2 !   76.6   0.1   1.1e-25   1.1e-25     437     517 .]     372     453 ..     368     453 .. 0.96

  Alignments for each domain:
  == domain 1  score: 382.0 bits;  conditional E-value: 2.8e-118
                          TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evvivf 75 
                                        Cgiagi++ k+++ke ++++ +m+++++hRGPD++g++       ail+h+RL+i+d ++g QPl++ + ++++ +
  lcl|FitnessBrowser__Btheta:350079   2 CGIAGILNIKTQTKELRDKALKMAQKIRHRGPDWSGIYVG---GSAILAHERLSIVDPQSGGQPLYSPDrKQALAV 74 
                                        ***************88********************999...8*************************999**** PP

                          TIGR01536  76 nGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYya 151
                                        nGEIYNh+++r+++  + y+F+t sD+EViLa+y+  g +++e++ G FAf+l+de+k+e+++aRD++G+ PLY +
  lcl|FitnessBrowser__Btheta:350079  75 NGEIYNHRDIRARYAGQ-YDFQTGSDCEVILALYKDKGIHFLEEISGIFAFVLYDEEKDEFLIARDPIGVIPLYIG 149
                                        ***************99.********************************************************** PP

                          TIGR01536 152 se.qgkllfaSEiKallalk.eikaeldkealaelltlqlvptektlfkevkelepakaldgeekleeywevekee 225
                                        ++ +gk++f+SE+Kal  ++ e +++l+++++ ++ +      ++ + +e+ ++e +k++  ++k++         
  lcl|FitnessBrowser__Btheta:350079 150 KDkDGKIYFGSELKALEGFCnEYEPFLPGHYFYSKEGKM----KRWYTREWTDYESVKDN--DAKVS--------- 210
                                        **99****************99************99998....5799*********9997..44444......... PP

                          TIGR01536 226 vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak.............sevktFsigfe 288
                                                  +++e+ledav+++l++dvp+gvllSGGlDSs+++aiakk+a+              ++++F+ig++
  lcl|FitnessBrowser__Btheta:350079 211 ----------DVKEALEDAVHRQLMSDVPYGVLLSGGLDSSVISAIAKKYAAkrietdgasdawwPQLHSFAIGLK 276
                                        ..........5***************************************999************9********** PP

                          TIGR01536 289 dskdldeskaarkvadelgtehkevliseeevlkeleevilale..eptairasiplyllsklarekgvkVvLsGe 362
                                        + +dl     ar+va+++gt h+e+  + +e+l+++++vi+ +e  ++t++ras+p+yll++ ++ +g+k+vLsGe
  lcl|FitnessBrowser__Btheta:350079 277 GAPDLI---KAREVAEYIGTVHHEINYTVQEGLDAIRDVIYFIEtyDVTTVRASTPMYLLARVIKSMGIKMVLSGE 349
                                        999999...9****************************************************************** PP

                          TIGR01536 363 GaDElfgGYeyfreakaeeale 384
                                        GaDE+fgGY yf++a+  ++++
  lcl|FitnessBrowser__Btheta:350079 350 GADEVFGGYLYFHKAPTPKDFH 371
                                        *****************99998 PP

  == domain 2  score: 76.6 bits;  conditional E-value: 1.1e-25
                          TIGR01536 437 eellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr..dgkeKvlLreaaeellPeeil 510
                                        ee++r+  +l+++d+lra+ + ++a+++E RvPflDke++++a+ ++p++k+   ++ eK++ rea++++lPe+++
  lcl|FitnessBrowser__Btheta:350079 372 EETVRKLSKLHMYDCLRAN-KSLSAWGVEGRVPFLDKEFLDVAMALNPKAKMCpgKEIEKRIVREAFADMLPESVA 446
                                        78899999***********.****************************9999888999****************** PP

                          TIGR01536 511 eRkKeaf 517
                                        +R+Ke+f
  lcl|FitnessBrowser__Btheta:350079 447 WRQKEQF 453
                                        *****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (559 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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 3.40
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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