Alignments for a candidate for asnB in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Escherichia coli BW25113

Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate 14804 b0674 asparagine synthetase B (NCBI)

Query= CharProtDB::CH_002444
         (554 letters)



>FitnessBrowser__Keio:14804
          Length = 554

 Score = 1130 bits (2922), Expect = 0.0
 Identities = 554/554 (100%), Positives = 554/554 (100%)

Query: 1   MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60
           MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA
Sbjct: 1   MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60

Query: 61  QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120
           QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG
Sbjct: 61  QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120

Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180
           MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY
Sbjct: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180

Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240
           LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS
Sbjct: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240

Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300
           SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF
Sbjct: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300

Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360
           TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY
Sbjct: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360

Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420
           FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD
Sbjct: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420

Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480
           KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET
Sbjct: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480

Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540
           ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD
Sbjct: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540

Query: 541 PSGRAVGVHQSAYK 554
           PSGRAVGVHQSAYK
Sbjct: 541 PSGRAVGVHQSAYK 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: 1194
Number of extensions: 29
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 14804 b0674 (asparagine synthetase B (NCBI))
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.2128.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.7e-157  510.0   0.4   4.6e-132  427.5   0.1    2.3  2  lcl|FitnessBrowser__Keio:14804  b0674 asparagine synthetase B (N


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14804  b0674 asparagine synthetase B (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.5   0.1  4.6e-132  4.6e-132       1     384 [.       2     371 ..       2     376 .. 0.97
   2 !   82.2   0.1   2.1e-27   2.1e-27     436     517 .]     371     453 ..     368     453 .. 0.94

  Alignments for each domain:
  == domain 1  score: 427.5 bits;  conditional E-value: 4.6e-132
                       TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evvivfnGE 78 
                                     C+i+g++d k++a+e ++++ e++++++hRGPD++g++ +   +nail+h+RL+i+d+++gaQPl+n++ + v+ +nGE
  lcl|FitnessBrowser__Keio:14804   2 CSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYAS---DNAILAHERLSIVDVNAGAQPLYNQQkTHVLAVNGE 77 
                                     ***************8899*******************99...8*************************999******* PP

                       TIGR01536  79 IYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYyase.qgk 156
                                     IYNh++Lr+e+ ++ y+F+t sD+EViLa+y+e g e++++L+GmFAfal+d++k+++++ RD+lGi PLY++++ +g+
  lcl|FitnessBrowser__Keio:14804  78 IYNHQALRAEYGDR-YQFQTGSDCEVILALYQEKGPEFLDDLQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDeHGQ 155
                                     **************.************************************************************9*** PP

                       TIGR01536 157 llfaSEiKallalk.eikaeldkealaelltlqlvptektlfkevkelepakaldgeekleeywevekeevkeseeelv 234
                                     l++aSE+Kal++++ +ik+++ +++l+++ ++      +++++++++++++k++ +++k+                   
  lcl|FitnessBrowser__Keio:14804 156 LYVASEMKALVPVCrTIKEFPAGSYLWSQDGEIR----SYYHRDWFDYDAVKDN-VTDKN------------------- 210
                                     ********************************94....7*************98.54444................... PP

                       TIGR01536 235 eelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak.............sevktFsigfedskdldeskaar 300
                                      elr++led+vk++l++dvp+gvllSGGlDSs+++ai+kk+a+              ++++F++g+++s+dl+   aa+
  lcl|FitnessBrowser__Keio:14804 211 -ELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAArrvedqerseawwPQLHSFAVGLPGSPDLK---AAQ 285
                                     .49***************************************99************9****************...*** PP

                       TIGR01536 301 kvadelgtehkevliseeevlkeleevilale..eptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfrea 377
                                     +va++lgt h+e++++ +e+l+++++vi+++e  ++t+iras+p+yl+s++++++g+k+vLsGeG+DE+fgGY yf++a
  lcl|FitnessBrowser__Keio:14804 286 EVANHLGTVHHEIHFTVQEGLDAIRDVIYHIEtyDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHKA 364
                                     ******************************************************************************* PP

                       TIGR01536 378 kaeeale 384
                                     +++++l+
  lcl|FitnessBrowser__Keio:14804 365 PNAKELH 371
                                     ****998 PP

  == domain 2  score: 82.2 bits;  conditional E-value: 2.1e-27
                       TIGR01536 436 leellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr..dgkeKvlLreaaeellPeeileR 512
                                      ee++r+ l+l+++d+ ra+ ++++a+++E+RvPflDk+++++a++i+p+ k+    ++eK++Lre++e++lP ++++R
  lcl|FitnessBrowser__Keio:14804 371 HEETVRKLLALHMYDCARAN-KAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCgnGKMEKHILRECFEAYLPASVAWR 448
                                     689999**************.****************************8888666889******************** PP

                       TIGR01536 513 kKeaf 517
                                     +Ke+f
  lcl|FitnessBrowser__Keio:14804 449 QKEQF 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 0.01s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 5.26
//
[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