Alignments for a candidate for asnB in Desulfotalea psychrophila LSv54

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Desulfotalea psychrophila LSv54

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_011187278.1 DP_RS00145 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000025945.1:WP_011187278.1
          Length = 634

 Score =  311 bits (797), Expect = 6e-89
 Identities = 198/644 (30%), Positives = 331/644 (51%), Gaps = 57/644 (8%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGF--RRLSIIDV 58
           MCG  G FN   +A        ++ M + I HRGPD+ G ++D   G G    RL+I+D+
Sbjct: 1   MCGLAGFFNYQFIADNTILH--LQSMGKSISHRGPDASGTWYDADTGIGLVHTRLAIVDL 58

Query: 59  ENGG-QPLSYEDETYWIIFNGEIYNYIELREELEAKGYT--FNTDSDTEVLLATYRHYKE 115
            + G QP+  + + Y I FNGEIYN++ LR++LE       +   SDTE LLA +  +  
Sbjct: 59  SSAGHQPMHSQCDRYVIAFNGEIYNHLMLRQKLEQANQAPAWRGHSDTETLLACFVAWGI 118

Query: 116 EAASKLR-GMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQN-D 173
           E   K+  GMFA  +W+K +  L  ARD  G KPLY+    D + F SE K+L    +  
Sbjct: 119 EQTLKVTVGMFALALWDKQEQNLTLARDRAGEKPLYWGWQGDTLLFGSELKALKAHPDFK 178

Query: 174 IEIDKEALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDI---TFKTYFKAN---- 226
            ++ ++AL  YM   ++  P ++   + K+ PG   T+    +I   T K Y+  N    
Sbjct: 179 AKVSRDALAVYMRHNYISAPQSIYEGIYKLLPGHYVTLNSVSNIDTATPKAYWTMNQAIE 238

Query: 227 ---FKPVQTEEDKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVA-KEFHPS 282
               +P    + + V  +   +  S+   M +DVP+G+FLSGG+DSS +V++  K+   S
Sbjct: 239 SGIAQPFSGTDIEAVDLLEHRLSQSIGGQMLADVPLGAFLSGGVDSSVVVALMQKQAQQS 298

Query: 283 LKTFSVGFEQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAA 342
           +KT+++GF+   ++E   A   A  LG E+    +S ++ +  +P++   + +P AD + 
Sbjct: 299 VKTYAIGFDDPRYNEAQYAAAVARHLGTEHTELYVSAQDALELVPQLPSIYCEPFADSSQ 358

Query: 343 IPLYFVAKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVM 402
           +P + V K A++HVTVALSG+G DELFGGY  Y                     ++    
Sbjct: 359 LPTFLVTKMARQHVTVALSGDGGDELFGGYTPYL--------------FTPRYWNLLKCY 404

Query: 403 PEGMRGKSLLERGCTPLQDRYIGNAKIF----EESVKKQLLKHYNPNLSYRDV------- 451
           P+ +R          PL D+++  A++     +ES  + ++ H+       DV       
Sbjct: 405 PQPLRAALAASMSRLPLPDKFLKLAEVMGASNKESFYRSIMSHWG---QPEDVVIGAKEP 461

Query: 452 -----TKTYFTESSSYSDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVF 506
                +   + E+ S+   + M  ++   +M  DIL+K D+  MANSLE RVP LD  V 
Sbjct: 462 ASVLNSSDLWPETDSFE--HWMMAMEAQMYMPDDILVKVDRAAMANSLETRVPLLDHRVI 519

Query: 507 DVASKIPDELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNI 566
           ++A ++P  +K ++G  K++LR+     VP  ++ R K GF +P+ +WL+  + +W   +
Sbjct: 520 ELAWQLPLSMKIRDGKGKWVLREVLYRHVPRELIERPKKGFSIPLANWLRGPLRDWAEAL 579

Query: 567 IQESQT--DAYIHKDYVLQLLEDHCADKADNSRKIWTVLIFMIW 608
           + E +   + Y +   + +  + H   K DN+ K+W+VL+F  W
Sbjct: 580 LDEKRLRGEGYFYPAPIREAWQQHVQGKRDNASKLWSVLMFQAW 623


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: 961
Number of extensions: 58
Number of successful extensions: 8
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: 632
Length of database: 634
Length adjustment: 38
Effective length of query: 594
Effective length of database: 596
Effective search space:   354024
Effective search space used:   354024
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_011187278.1 DP_RS00145 (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.3825454.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.2e-146  473.5   0.0   6.1e-146  473.3   0.0    1.0  1  NCBI__GCF_000025945.1:WP_011187278.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025945.1:WP_011187278.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.3   0.0  6.1e-146  6.1e-146       1     517 []       2     560 ..       2     560 .. 0.88

  Alignments for each domain:
  == domain 1  score: 473.3 bits;  conditional E-value: 6.1e-146
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.ev 71 
                                           Cg+ag+++++  a+++   +++m + ++hRGPDa+g+w d  +++ +l+h RLai+dls++ +QP++++  ++
  NCBI__GCF_000025945.1:WP_011187278.1   2 CGLAGFFNYQFIADNTILHLQSMGKSISHRGPDASGTWYD-ADTGIGLVHTRLAIVDLSSAgHQPMHSQCdRY 73 
                                           *********999999999**********************.79***************9999*******99** PP

                             TIGR01536  72 vivfnGEIYNheeLreeleekGy..eFetksDtEViLaayeewg.eelverLeGmFAfalwdekkgelflaRD 141
                                           vi fnGEIYNh  Lr++le++     ++++sDtE +La + +wg e++++   GmFA+alwd+++++l laRD
  NCBI__GCF_000025945.1:WP_011187278.1  74 VIAFNGEIYNHLMLRQKLEQANQapAWRGHSDTETLLACFVAWGiEQTLKVTVGMFALALWDKQEQNLTLARD 146
                                           ******************98744227*********************************************** PP

                             TIGR01536 142 rlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal..... 209
                                           r G kPLY + ++++llf+SE+Kal a++++ka++ ++ala ++ +++ + ++++++++++l p++++     
  NCBI__GCF_000025945.1:WP_011187278.1 147 RAGEKPLYWGWQGDTLLFGSELKALKAHPDFKAKVSRDALAVYMRHNYISAPQSIYEGIYKLLPGHYVtlnsv 219
                                           ***********************************************99*******************88554 PP

                             TIGR01536 210 .dgeeklee.....ywevekee.......vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslva 269
                                            +    +++     yw +++         ++ ++ e+v+ l++ l +++  ++ advp+g++lSGG+DSs+v+
  NCBI__GCF_000025945.1:WP_011187278.1 220 sN----IDTatpkaYWTMNQAIesgiaqpFSGTDIEAVDLLEHRLSQSIGGQMLADVPLGAFLSGGVDSSVVV 288
                                           41....33345567****99878999999999999************************************** PP

                             TIGR01536 270 aiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasip 342
                                           a+++k+a+++vkt++igf+ ++ ++e+++a++va++lgteh+e+++s++++l+ ++++  +  ep+a++++ p
  NCBI__GCF_000025945.1:WP_011187278.1 289 ALMQKQAQQSVKTYAIGFD-DPRYNEAQYAAAVARHLGTEHTELYVSAQDALELVPQLPSIYCEPFADSSQLP 360
                                           *******************.9**************************************************** PP

                             TIGR01536 343 lyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale.........................lpease 390
                                           ++l++k+ar++ v+V+LsG+G+DElfgGY  +   ++  +++                         +     
  NCBI__GCF_000025945.1:WP_011187278.1 361 TFLVTKMARQH-VTVALSGDGGDELFGGYTPYLFTPR--YWNllkcypqplraalaasmsrlplpdkF----- 425
                                           ***********.*********************9755..45544787777777764444444433331..... PP

                             TIGR01536 391 laekkl............llqaklakeselkellkakleeelkekeelkkelkeeseleellrldlelllsdl 451
                                                l              ++++++++ + e +    +e  +  ++ +   +++s  + ++  +++ +++d+
  NCBI__GCF_000025945.1:WP_011187278.1 426 -----LklaevmgasnkeSFYRSIMSHWGQPEDVVIGAKEPASVLNSSDLWPETDSFEHWMMAMEAQMYMPDD 493
                                           .....13333223322334445555555555555544444444444333333334666778999********* PP

                             TIGR01536 452 lrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           +++k Dr++ma+slE RvP+lD++++ela+++p ++k+rdgk K++Lre++ +++P+e+ eR+K++f
  NCBI__GCF_000025945.1:WP_011187278.1 494 ILVKvDRAAMANSLETRVPLLDHRVIELAWQLPLSMKIRDGKGKWVLREVLYRHVPRELIERPKKGF 560
                                           ****************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (634 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: 00:00:00.01
# Mc/sec: 29.96
//
[ok]

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