Alignments for a candidate for asnB in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Shewanella amazonensis SB2B

Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate 6937968 Sama_2101 asparagine synthetase B (RefSeq)

Query= CharProtDB::CH_002444
         (554 letters)



>FitnessBrowser__SB2B:6937968
          Length = 554

 Score =  795 bits (2053), Expect = 0.0
 Identities = 388/554 (70%), Positives = 451/554 (81%), Gaps = 1/554 (0%)

Query: 1   MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60
           MCSIF + DI++DA  +R+ ALE+S+L+RHRGPDWSGIYA D+A+LAHERL+IVD+  GA
Sbjct: 1   MCSIFAILDIQSDASAMRQVALEMSKLLRHRGPDWSGIYADDHAVLAHERLAIVDIEHGA 60

Query: 61  QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120
           QPL +   + VLAVNGEIYNH+ L+AE GD+Y +QT SDCEVILALYQE G +FLD L G
Sbjct: 61  QPLISDDGSLVLAVNGEIYNHKELKAELGDKYSYQTNSDCEVILALYQEYGSDFLDKLNG 120

Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180
           +FAF LYD  K  YLIGRDH+GIIPLY G D  G  YVASEMKALVPVC+T++ F  G Y
Sbjct: 121 IFAFVLYDKAKGTYLIGRDHIGIIPLYTGRDAKGNFYVASEMKALVPVCKTVETFAPGHY 180

Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240
           L S D +   YY RDW  +DAV DN     ELR ALE +VK  LMSDVPYGVLLSGGLDS
Sbjct: 181 LSSTDAQPVRYYQRDWQAFDAVVDNEASVEELRGALEAAVKRQLMSDVPYGVLLSGGLDS 240

Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300
           SI+SAIT+ +A RR+ED + SEAWWPQLHSFAVGL GSPDL A+++VA+ +GT+HHEIHF
Sbjct: 241 SIVSAITQTFAKRRIEDNDESEAWWPQLHSFAVGLKGSPDLAASRKVADAIGTIHHEIHF 300

Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360
           T QEGLDAI+DVIYH+ETYDVTTIRA+TPMYLM+RKIKAMGIKMVLSGEG+DE+FGGYLY
Sbjct: 301 TFQEGLDAIKDVIYHLETYDVTTIRAATPMYLMARKIKAMGIKMVLSGEGADELFGGYLY 360

Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420
           FHKAPN +  HEE VRKL  LH++DC RANKAM+AWG+EARVPFLDK+F+DVAMR+NP  
Sbjct: 361 FHKAPNPQAFHEELVRKLDKLHLFDCLRANKAMAAWGLEARVPFLDKEFMDVAMRLNPAA 420

Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480
           KM G GK+EKHILRE FE  LPA +AWRQKEQFSDGVGYSWID LKE AA QV D QL  
Sbjct: 421 KMSGKGKIEKHILREAFEHKLPAEIAWRQKEQFSDGVGYSWIDGLKEQAAAQVDDLQLAN 480

Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540
           ARFRFP+NTP +KEAY YR  FEELFPL SAA  VPGG SVACS+ +A+ WD + + + D
Sbjct: 481 ARFRFPHNTPETKEAYFYRCFFEELFPLESAALTVPGGKSVACSTPEALAWDASLQGIID 540

Query: 541 PSGRAV-GVHQSAY 553
           PSGRAV  VH  +Y
Sbjct: 541 PSGRAVREVHAQSY 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: 907
Number of extensions: 30
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: 554
Length adjustment: 36
Effective length of query: 518
Effective length of database: 518
Effective search space:   268324
Effective search space used:   268324
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 6937968 Sama_2101 (asparagine synthetase B (RefSeq))
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.28306.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.3e-149  482.6   0.5   7.4e-124  400.5   0.0    2.9  2  lcl|FitnessBrowser__SB2B:6937968  Sama_2101 asparagine synthetase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937968  Sama_2101 asparagine synthetase B (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.5   0.0  7.4e-124  7.4e-124       1     385 [.       2     372 ..       2     382 .. 0.96
   2 !   79.4   0.2   1.4e-26   1.4e-26     437     517 .]     372     453 ..     369     453 .. 0.94

  Alignments for each domain:
  == domain 1  score: 400.5 bits;  conditional E-value: 7.4e-124
                         TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evvivfn 76 
                                       C+i++i+d + +a+  ++ + em+++l+hRGPD++g++ d   ++a+l+h+RLai+d+++gaQPl +++ + v+ +n
  lcl|FitnessBrowser__SB2B:6937968   2 CSIFAILDIQSDASAMRQVALEMSKLLRHRGPDWSGIYAD---DHAVLAHERLAIVDIEHGAQPLISDDgSLVLAVN 75 
                                       ************99999***********************...8************************99******* PP

                         TIGR01536  77 GEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYyase 153
                                       GEIYNh+eL++el +k y+++t+sD+EViLa+y+e+g +++++L+G FAf+l+d++kg++++ RD++Gi PLY +++
  lcl|FitnessBrowser__SB2B:6937968  76 GEIYNHKELKAELGDK-YSYQTNSDCEVILALYQEYGSDFLDKLNGIFAFVLYDKAKGTYLIGRDHIGIIPLYTGRD 151
                                       ****************.************************************************************ PP

                         TIGR01536 154 .qgkllfaSEiKallalk.eikaeldkealaelltlqlvptektlfkevkelepakaldgeekleeywevekeevke 228
                                        +g++++aSE+Kal++++ +++++ ++++l+++ +  +    ++++++++ ++++ ++  e+               
  lcl|FitnessBrowser__SB2B:6937968 152 aKGNFYVASEMKALVPVCkTVETFAPGHYLSSTDAQPV----RYYQRDWQAFDAVVDN--EA--------------- 207
                                       9*****************99**********99998885....799*****99999886..33............... PP

                         TIGR01536 229 seeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak.............sevktFsigfedskd 292
                                           +veelr +le+avk++l++dvp+gvllSGGlDSs+v+ai++ +ak              ++++F++g+++s+d
  lcl|FitnessBrowser__SB2B:6937968 208 ----SVEELRGALEAAVKRQLMSDVPYGVLLSGGLDSSIVSAITQTFAKrriedndeseawwPQLHSFAVGLKGSPD 280
                                       ....4567******************************************************9************** PP

                         TIGR01536 293 ldeskaarkvadelgtehkevliseeevlkeleevilale..eptairasiplyllsklarekgvkVvLsGeGaDEl 367
                                       l    a rkvad++gt h+e++++ +e+l+++++vi++le  ++t+ira++p+yl++++++++g+k+vLsGeGaDEl
  lcl|FitnessBrowser__SB2B:6937968 281 LA---ASRKVADAIGTIHHEIHFTFQEGLDAIKDVIYHLEtyDVTTIRAATPMYLMARKIKAMGIKMVLSGEGADEL 354
                                       **...************************************************************************ PP

                         TIGR01536 368 fgGYeyfreakaeealel 385
                                       fgGY yf++a++ +a++ 
  lcl|FitnessBrowser__SB2B:6937968 355 FGGYLYFHKAPNPQAFHE 372
                                       ***************983 PP

  == domain 2  score: 79.4 bits;  conditional E-value: 1.4e-26
                         TIGR01536 437 eellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr..dgkeKvlLreaaeellPeeile 511
                                       eel+r+  +l+l d+lra+ ++++a++lE+RvPflDke++++a++++p +k++   + eK++Lrea+e+ lP ei++
  lcl|FitnessBrowser__SB2B:6937968 372 EELVRKLDKLHLFDCLRAN-KAMAAWGLEARVPFLDKEFMDVAMRLNPAAKMSgkGKIEKHILREAFEHKLPAEIAW 447
                                       67788888999********.****************************9999987899******************* PP

                         TIGR01536 512 RkKeaf 517
                                       R+Ke+f
  lcl|FitnessBrowser__SB2B:6937968 448 RQKEQF 453
                                       ****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (554 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 0.00s 00:00:00.05 Elapsed: 00:00:00.06
# Mc/sec: 4.37
//
[ok]

This GapMind analysis is from Apr 09 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