Alignments for a candidate for asnB in Desulfovibrio oxyclinae DSM 11498

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Desulfovibrio oxyclinae DSM 11498

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_026167487.1 B149_RS0106715 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000375485.1:WP_026167487.1
          Length = 646

 Score =  316 bits (810), Expect = 2e-90
 Identities = 209/651 (32%), Positives = 341/651 (52%), Gaps = 53/651 (8%)

Query: 1   MCGFVGVFNKHPLAQTADQEEL---IKQMNQMIVHRGPDSDGYFHDEHVGFGF--RRLSI 55
           MCG  G+ +   +A+    +EL   +++M   ++HRGPD  G   DE  G     RRL+I
Sbjct: 1   MCGIAGILD---IARRTGADELRTRVRRMADTLIHRGPDGHGLHVDELQGLAMAHRRLAI 57

Query: 56  IDVENGG-QPLSYEDETYWIIFNGEIYNYIELREELEAKGYTF---NTDSDTEVLLATYR 111
           ID+ + G QP+      + ++ NGEIYN+ +LR +L+ +G  F      SDTEVLLA   
Sbjct: 58  IDLSDAGAQPMLSRSGRFALVLNGEIYNFHQLRADLQDEGGPFLPWRGGSDTEVLLAAIE 117

Query: 112 HYKEEAASKLR-GMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVA 170
            +  E A +   GMFAF +W+  +  L  ARD  G KPLY++   ++  FASE K+L  A
Sbjct: 118 AWGVEGALRRAIGMFAFAVWDTRERQLILARDRMGEKPLYWSLDGNRFLFASELKAL-TA 176

Query: 171 QNDI--EIDKEALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKAN-- 226
             D   +++ EA+  ++ +Q+VP P  +   V K+EPG+  T+ P G +  K Y++ +  
Sbjct: 177 HPDFSRQVNPEAVSLFLRYQYVPAPHCIWQGVHKLEPGTMLTVLPYGQVQTKAYWRLHDV 236

Query: 227 -----FKPVQTEEDKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHP 281
                 +P +   +    E+ + + ++V + + SDVP+G+ LSGGIDSS I ++A++   
Sbjct: 237 VSQGGLEPFEGSRELAAAELEELLTEAVGMQLESDVPLGTLLSGGIDSSLITALARKVSD 296

Query: 282 S-LKTFSVGFEQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADP 340
           S ++TF++G++   F E   A++ A  LG E+   ++SP+E ++ LP +   +D+P AD 
Sbjct: 297 SPVRTFTIGYDDPAFDESAQARKIAEYLGTEHTELIVSPDEALDLLPNLPDMWDEPFADA 356

Query: 341 AAIPLYFVAKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVA- 399
           + +P   V++  ++HVTV LSG+G DE FGGYN  R   + K + R+ SGL   L     
Sbjct: 357 SMLPTALVSRLTREHVTVCLSGDGGDETFGGYN--RHVTAPKLWSRL-SGLPLPLRRAVS 413

Query: 400 -AVMPEGMRGKSLLERGCTPL--QDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTY- 455
            A+     R    L     PL    R + N       + + + + +   L Y  +  T+ 
Sbjct: 414 RAIHSASPRKLDSLYAFWEPLLPSSRRMNNPGFKLHKLARVMTQPHREGL-YAALCSTWD 472

Query: 456 ----------------FTESSSYSDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVP 499
                             E  S+ +   MQY D  +++ GDIL K D+  MA  LE R P
Sbjct: 473 RPEELTGVPAPPLQAQAPEGLSFRE--WMQYQDSLSYLPGDILTKVDRAAMAVGLESRAP 530

Query: 500 FLDKVVFDVASKIPDELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEM 559
           +LD  V + A ++P+  K  +G  K +LR   +  VP  + +R K+GF VP+  WL+  +
Sbjct: 531 YLDHRVVEFAWRLPESYKVAHGRGKLVLRDILDKHVPRELTDRPKMGFGVPLGEWLRGPL 590

Query: 560 NEWVRNIIQESQTDAYIHKD--YVLQLLEDHCADKADNSRKIWTVLIFMIW 608
            +W R+ +   + +  I ++   V + L DH + + DN   +W VL+   W
Sbjct: 591 RDWTRDTLHPKKLEQGILENGVPVARALNDHMSGRRDNEYALWGVLMLQSW 641


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: 992
Number of extensions: 48
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: 646
Length adjustment: 38
Effective length of query: 594
Effective length of database: 608
Effective search space:   361152
Effective search space used:   361152
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_026167487.1 B149_RS0106715 (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.2754287.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-145  471.6   0.0   2.4e-145  471.3   0.0    1.1  1  NCBI__GCF_000375485.1:WP_026167487.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000375485.1:WP_026167487.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  471.3   0.0  2.4e-145  2.4e-145       1     517 []       2     578 ..       2     578 .. 0.89

  Alignments for each domain:
  == domain 1  score: 471.3 bits;  conditional E-value: 2.4e-145
                             TIGR01536   1 Cgiagivdlkakake..eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek. 69 
                                           Cgiagi+d  + +     +  +++m++tl hRGPD++g++ d + ++ +++hrRLaiidls++ aQP+ +++ 
  NCBI__GCF_000375485.1:WP_026167487.1   2 CGIAGILDIARRTGAdeLRTRVRRMADTLIHRGPDGHGLHVD-ELQGLAMAHRRLAIIDLSDAgAQPMLSRSg 73 
                                           *******99877655556799*********************.689***************999********* PP

                             TIGR01536  70 evvivfnGEIYNheeLreeleekGyeF...etksDtEViLaayeewg.eelverLeGmFAfalwdekkgelfl 138
                                           + ++v nGEIYN+++Lr++l+++G  F   ++ sDtEV+Laa+e+wg e ++ r  GmFAfa+wd+++++l+l
  NCBI__GCF_000375485.1:WP_026167487.1  74 RFALVLNGEIYNFHQLRADLQDEGGPFlpwRGGSDTEVLLAAIEAWGvEGALRRAIGMFAFAVWDTRERQLIL 146
                                           ************************87755599***************************************** PP

                             TIGR01536 139 aRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal.. 209
                                           aRDr+G kPLY + +++++lfaSE+Kal+a++++ ++++ ea++ +l +q+vp +++++++v++lep+  l  
  NCBI__GCF_000375485.1:WP_026167487.1 147 ARDRMGEKPLYWSLDGNRFLFASELKALTAHPDFSRQVNPEAVSLFLRYQYVPAPHCIWQGVHKLEPGTMLtv 219
                                           **********************************************************************999 PP

                             TIGR01536 210 ..dgeekleeywevekee.......vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiak 273
                                             +g+ + + yw++++         ++ s e + +el+ell++av ++l +dvp+g+llSGG+DSsl++a+a+
  NCBI__GCF_000375485.1:WP_026167487.1 220 lpYGQVQTKAYWRLHDVVsqgglepFEGSRELAAAELEELLTEAVGMQLESDVPLGTLLSGGIDSSLITALAR 292
                                           9988888888***999888899999999********************************************* PP

                             TIGR01536 274 keaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyll 346
                                           k ++s+v+tF+ig++ ++++des++ark+a++lgteh+e+++s++e+l+ l+++  +++ep+a++++ p+ l+
  NCBI__GCF_000375485.1:WP_026167487.1 293 KVSDSPVRTFTIGYD-DPAFDESAQARKIAEYLGTEHTELIVSPDEALDLLPNLPDMWDEPFADASMLPTALV 364
                                           ***************.********************************************************* PP

                             TIGR01536 347 sklarekgvkVvLsGeGaDElfgGYeyfreakaeeale................................... 384
                                           s+l+re+ v+V LsG+G+DE fgGY+++ +a++   +                                    
  NCBI__GCF_000375485.1:WP_026167487.1 365 SRLTREH-VTVCLSGDGGDETFGGYNRHVTAPK--LWSrlsglplplrravsraihsasprkldslyafwepl 434
                                           *******.********************99854..34344689988888777666666666666665555555 PP

                             TIGR01536 385 lpeaselaekkl............llqaklakeselkellkakleeelkekeelkkelkee...seleellrl 442
                                           lp +++     +            ++++  ++    +    ++ +eel+ + +   + ++    s  e ++++
  NCBI__GCF_000375485.1:WP_026167487.1 435 LPSSRR-----MnnpgfklhklarVMTQPHREGLYAALCSTWDRPEELTGVPAPPLQAQAPeglSFREWMQYQ 502
                                           333333.....0333335554443333333333444444556666666655554333333356788899**** PP

                             TIGR01536 443 dlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkK 514
                                           d   +l+++++ k Dr++ma +lE+R+P+lD+++ve+a+++p ++k+ +g+ K +Lr ++++++P+e+ +R+K
  NCBI__GCF_000375485.1:WP_026167487.1 503 DSLSYLPGDILTKvDRAAMAVGLESRAPYLDHRVVEFAWRLPESYKVAHGRGKLVLRDILDKHVPRELTDRPK 575
                                           ************************************************************************* PP

                             TIGR01536 515 eaf 517
                                           ++f
  NCBI__GCF_000375485.1:WP_026167487.1 576 MGF 578
                                           *99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (646 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 35.83
//
[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