Alignments for a candidate for asnB in Desulfobacca acetoxidans DSM 11109

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Desulfobacca acetoxidans DSM 11109

Align Putative asparagine synthetase [glutamine-hydrolyzing] 2; EC 6.3.5.4 (uncharacterized)
to candidate WP_083800296.1 DESAC_RS13250 asparagine synthase (glutamine-hydrolyzing)

Query= curated2:Q58456
         (515 letters)



>NCBI__GCF_000195295.1:WP_083800296.1
          Length = 641

 Score =  204 bits (518), Expect = 1e-56
 Identities = 149/477 (31%), Positives = 239/477 (50%), Gaps = 43/477 (9%)

Query: 1   MCGINGIIRFGKEVIKEEINKMNKAIKHRGPDDEGIFIYNFKNYSIGLGHVRLAILDLSE 60
           MCGI G I      +  E+++     KHRGPD  G       ++ IGL H RL+I+DLS+
Sbjct: 19  MCGIAGFISNNNNNL--ELSQAESIQKHRGPDASGCLYLQVGDWHIGLAHQRLSIIDLSD 76

Query: 61  KGHQPMGYNVDEDKIIYRDDELDRADIIIVYNGEIYNYLELK---EKFNLETETGTDTEV 117
            G+QPM     +  IIY              NGE+YNYLE++   E+  L+  + +DTEV
Sbjct: 77  AGNQPMAAADGQSWIIY--------------NGEVYNYLEIRAELEQAGLQFHSTSDTEV 122

Query: 118 ILKLYNKLGFD-CVKEFNGMWAFCIFDKKKGLIFCSRDRLGVKPFYYYWDGNEFIFSSEL 176
           IL      G +  + +FNGMWAF   D     +  SRDR+GVKP YY++   +  F+SE+
Sbjct: 123 ILAALQYWGPEKALPKFNGMWAFAYLDGPHNRLILSRDRVGVKPLYYFFSERQLYFASEI 182

Query: 177 KGILAVKEINKKENINKDAVELYFALGFIPSP-YSIYKNTFKLEARQNLIFDLDKREIRK 235
           K IL +  +  + ++N   +  Y     + +   + +    K+ A   +  DL    +  
Sbjct: 183 KTILTM--VGGRFSLNYQVIGKYLLQSLLETDNQTFFAGIAKVPAAHLVEIDLASPSLSL 240

Query: 236 YY--YWELPDYKPIYDK-KKLIEEGKKLLYDAVKIRMRSDVPVGAFLSGGLDSSTVVGVM 292
            +  YW L   +P  D  + +++E + L +DAV++R+RSDVP+G  LSGG+DSS +   M
Sbjct: 241 TFKPYWRLHFAEPPNDAGEGILKEVQDLFFDAVRLRLRSDVPLGILLSGGVDSSAIAVAM 300

Query: 293 REF----TDLSKLHTFSIGFEGKYDETPYIKIVVDYFKTQHHHYY--FKERDFEELIDKY 346
           ++      +L+ L   ++  + ++DE+ YI IV        H     F+     + ++K 
Sbjct: 301 QQVLGPGANLNLLS--AVSRDHRFDESQYIDIVARRLDQPVHKVMLDFQPSQAFDYLEKV 358

Query: 347 SWIYDEPFGDYSGFPTYKVSEMARKF-VTVVLSGDGGDEVFGGYMTHLNGYRMDFIRK-- 403
            W  DEP   ++    Y + + A++  +TVVLSG GGDE+  GY  +L  Y    +R+  
Sbjct: 359 CWFNDEPVYSFAVVSQYLLMQKAKELGITVVLSGQGGDELLCGYKKYLGFYIQSLLRQGH 418

Query: 404 LPKFLRVVGSKLPVKKDLNGIANLYLLKEAFRL--SLINPEEFYAESIKEDAIRPEI 458
           +P  L+   S    ++D   +   + + EA R   S + P+E      K    +PEI
Sbjct: 419 IPTALKTFWSFW--RQDT--VLGQFSIMEAKRYLPSFLRPQELNIAGEKLKDFQPEI 471


Lambda     K      H
   0.322    0.144    0.434 

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: 842
Number of extensions: 56
Number of successful extensions: 5
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: 515
Length of database: 641
Length adjustment: 36
Effective length of query: 479
Effective length of database: 605
Effective search space:   289795
Effective search space used:   289795
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 (21.9 bits)
S2: 53 (25.0 bits)

Align candidate WP_083800296.1 DESAC_RS13250 (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.8795.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.5e-131  423.7   0.0   7.7e-131  423.5   0.0    1.0  1  lcl|NCBI__GCF_000195295.1:WP_083800296.1  DESAC_RS13250 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195295.1:WP_083800296.1  DESAC_RS13250 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.5   0.0  7.7e-131  7.7e-131       1     517 []      20     563 ..      20     563 .. 0.86

  Alignments for each domain:
  == domain 1  score: 423.5 bits;  conditional E-value: 7.7e-131
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkde.keenailghrRLaiidlseg.aQPlsn 67 
                                               Cgiag++ +++++     ++++    ++hRGPDa+g+   +  + + +l+h+RL+iidls++ +QP+++
  lcl|NCBI__GCF_000195295.1:WP_083800296.1  20 CGIAGFISNNNNN----LELSQAESIQKHRGPDASGCLYLQvGDWHIGLAHQRLSIIDLSDAgNQPMAA 84 
                                               ********97642....34555577889********75555599****************999****** PP

                                 TIGR01536  68 ek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewg.eelverLeGmFAfalwdekkg 134
                                               ++ +++i++nGE+YN+ e+r+ele++G +F+++sDtEViLaa+++wg e+++ +++Gm+Afa++d  ++
  lcl|NCBI__GCF_000195295.1:WP_083800296.1  85 ADgQSWIIYNGEVYNYLEIRAELEQAGLQFHSTSDTEVILAALQYWGpEKALPKFNGMWAFAYLDGPHN 153
                                               ***99**************************************************************** PP

                                 TIGR01536 135 elflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevke 202
                                               +l+l+RDr+G+kPLYy   + +l+faSEiK +l++   + +l+ +++ ++l  + l+++++t+f+++ +
  lcl|NCBI__GCF_000195295.1:WP_083800296.1 154 RLILSRDRVGVKPLYYFFSERQLYFASEIKTILTMVGGRFSLNYQVIGKYLLQSlLETDNQTFFAGIAK 222
                                               ************************************999**********999999999*********** PP

                                 TIGR01536 203 lepakal.......dgeekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGl 263
                                               +++a+ +       + + +++ yw+++  e  ++  e   +e+++l+ dav+ rl++dvp+g+llSGG+
  lcl|NCBI__GCF_000195295.1:WP_083800296.1 223 VPAAHLVeidlaspSLSLTFKPYWRLHFAEpPNDAGEGILKEVQDLFFDAVRLRLRSDVPLGILLSGGV 291
                                               *****99999887666677777******996677788999***************************** PP

                                 TIGR01536 264 DSslvaaiakkeak..sevktFsigfedskdldeskaarkvadelgtehkevl..iseeevlkeleevi 328
                                               DSs++a+ +++ +   +++++ s     ++ +des+++  va+ l+   ++v+  +++ ++++ le+v 
  lcl|NCBI__GCF_000195295.1:WP_083800296.1 292 DSSAIAVAMQQVLGpgANLNLLSAVSR-DHRFDESQYIDIVARRLDQPVHKVMldFQPSQAFDYLEKVC 359
                                               *************99999999999988.9*****************9999875227899********** PP

                                 TIGR01536 329 laleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale...lpeaselaek 394
                                               +  +ep+   a++++yll+++a+e g++VvLsG+G+DEl+ GY+++  ++ +  l+   +p+a +    
  lcl|NCBI__GCF_000195295.1:WP_083800296.1 360 WFNDEPVYSFAVVSQYLLMQKAKELGITVVLSGQGGDELLCGYKKYLGFYIQSLLRqghIPTALK---- 424
                                               ****************************************************9999555333333.... PP

                                 TIGR01536 395 kl.........llqaklakeselkellkakl.eeelkekeelkkelkee.......seleellrldlel 446
                                               ++         l q +++   e k++l   l ++el+   e+ k+++ e        +l+e + ld ++
  lcl|NCBI__GCF_000195295.1:WP_083800296.1 425 TFwsfwrqdtvLGQFSIM---EAKRYLPSFLrPQELNIAGEKLKDFQPEilglsnnMTLQERQALDYQR 490
                                               223333332223332222...333333222202333333333333333355666668889999999999 PP

                                 TIGR01536 447 llsdllr.akDrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileR.k 513
                                               +    l  ++Dr+sma+  E+R PflD +l+e ++ +pp +klr+g +K+++r+a++  lP ei +R +
  lcl|NCBI__GCF_000195295.1:WP_083800296.1 491 FSIPILThFEDRMSMAWARELREPFLDYRLIEKIIPLPPRYKLRHGWTKYIFRQAMAPFLPPEITWRkD 559
                                               8877775156*********************************************************99 PP

                                 TIGR01536 514 Keaf 517
                                               K++f
  lcl|NCBI__GCF_000195295.1:WP_083800296.1 560 KQGF 563
                                               9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (641 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 14.15
//
[ok]

This GapMind analysis is from Apr 10 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