Alignments for a candidate for asnB in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Klebsiella michiganensis M5al

Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate BWI76_RS08180 BWI76_RS08180 asparagine synthase B

Query= CharProtDB::CH_002444
         (554 letters)



>FitnessBrowser__Koxy:BWI76_RS08180
          Length = 553

 Score = 1074 bits (2777), Expect = 0.0
 Identities = 520/553 (94%), Positives = 538/553 (97%)

Query: 1   MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60
           MCSIFGV DIKTDA ELRKKALELSRLMRHRGPDWSG+YA D AILAHERLSIVDVNAGA
Sbjct: 1   MCSIFGVLDIKTDAGELRKKALELSRLMRHRGPDWSGVYACDKAILAHERLSIVDVNAGA 60

Query: 61  QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120
           QPLYN  KTH LAVNGEIYNHQALRAEYGDRY FQTGSDCEVILALYQEKGP+FLDDLQG
Sbjct: 61  QPLYNAAKTHALAVNGEIYNHQALRAEYGDRYAFQTGSDCEVILALYQEKGPDFLDDLQG 120

Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180
           MFAFALYDSEKDAYLIGRDH+GIIPLYMG+DEHG  YVASEMKALVPVCRTIKEFPAGSY
Sbjct: 121 MFAFALYDSEKDAYLIGRDHIGIIPLYMGHDEHGNFYVASEMKALVPVCRTIKEFPAGSY 180

Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240
           LWS+DGEIR YY RDWFDYDAVKDNVTDKNELRQALE+SVKSHLMSDVPYGVLLSGGLDS
Sbjct: 181 LWSKDGEIREYYQRDWFDYDAVKDNVTDKNELRQALEESVKSHLMSDVPYGVLLSGGLDS 240

Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300
           S+ISAITKKYAARRVEDQE+SEAWWPQLHSFAVGL G+PDLKAAQEVANHLGTVHHEIHF
Sbjct: 241 SVISAITKKYAARRVEDQEKSEAWWPQLHSFAVGLEGAPDLKAAQEVANHLGTVHHEIHF 300

Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360
           TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY
Sbjct: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360

Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420
           FHKAPNAKELHEETVRKL ALHM+DCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD
Sbjct: 361 FHKAPNAKELHEETVRKLQALHMFDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420

Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480
           KMCGNGKMEKH+LRECFE+YLPASVAWRQKEQFSDGVGYSWIDTLKEVAA+Q+SDQQLET
Sbjct: 421 KMCGNGKMEKHVLRECFESYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAEQISDQQLET 480

Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540
           A FRFPYNTP+SKEAYLYREIFEELFP+PSAAECVPGGPSVACSSAKAIEWDE+FKKM+D
Sbjct: 481 ASFRFPYNTPSSKEAYLYREIFEELFPVPSAAECVPGGPSVACSSAKAIEWDESFKKMND 540

Query: 541 PSGRAVGVHQSAY 553
           PSGRAVGVHQSAY
Sbjct: 541 PSGRAVGVHQSAY 553


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: 1145
Number of extensions: 25
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: 553
Length adjustment: 36
Effective length of query: 518
Effective length of database: 517
Effective search space:   267806
Effective search space used:   267806
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 BWI76_RS08180 BWI76_RS08180 (asparagine synthase B)
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.23681.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   4.3e-152  493.6   0.5   3.5e-128  414.7   0.1    2.3  2  lcl|FitnessBrowser__Koxy:BWI76_RS08180  BWI76_RS08180 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS08180  BWI76_RS08180 asparagine synthase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.7   0.1  3.5e-128  3.5e-128       1     385 [.       2     372 ..       2     379 .. 0.97
   2 !   79.1   0.1   1.9e-26   1.9e-26     436     517 .]     371     453 ..     368     453 .. 0.93

  Alignments for each domain:
  == domain 1  score: 414.7 bits;  conditional E-value: 3.5e-128
                               TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.e 70 
                                             C+i+g++d k++a e ++++ e++++++hRGPD++gv+     ++ail+h+RL+i+d+++gaQPl+n++ +
  lcl|FitnessBrowser__Koxy:BWI76_RS08180   2 CSIFGVLDIKTDAGELRKKALELSRLMRHRGPDWSGVYAC---DKAILAHERLSIVDVNAGAQPLYNAAkT 69 
                                             ***************8899******************999...79************************99 PP

                               TIGR01536  71 vvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRD 141
                                              ++ +nGEIYNh++Lr+e+ ++ y F+t sD+EViLa+y+e g +++++L+GmFAfal+d++k+++++ RD
  lcl|FitnessBrowser__Koxy:BWI76_RS08180  70 HALAVNGEIYNHQALRAEYGDR-YAFQTGSDCEVILALYQEKGPDFLDDLQGMFAFALYDSEKDAYLIGRD 139
                                             9*********************.************************************************ PP

                               TIGR01536 142 rlGikPLYyase.qgkllfaSEiKallalk.eikaeldkealaelltlqlvptektlfkevkelepakald 210
                                             ++Gi PLY++ + +g++++aSE+Kal++++ +ik+++ +++l+++ ++      +++++++++++++k++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS08180 140 HIGIIPLYMGHDeHGNFYVASEMKALVPVCrTIKEFPAGSYLWSKDGEI----REYYQRDWFDYDAVKDN- 205
                                             ***********99***********************************9....48*************98. PP

                               TIGR01536 211 geekleeywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak.... 277
                                             +++k+                    elr++le++vk++l++dvp+gvllSGGlDSs+++ai+kk+a+    
  lcl|FitnessBrowser__Koxy:BWI76_RS08180 206 VTDKN--------------------ELRQALEESVKSHLMSDVPYGVLLSGGLDSSVISAITKKYAArrve 256
                                             54444....................49***************************************99*** PP

                               TIGR01536 278 .........sevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilale..eptai 337
                                                       ++++F++g+e+ +dl+   aa++va++lgt h+e++++ +e+l+++++vi+++e  ++t+i
  lcl|FitnessBrowser__Koxy:BWI76_RS08180 257 dqekseawwPQLHSFAVGLEGAPDLK---AAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIEtyDVTTI 324
                                             *********9****************...****************************************** PP

                               TIGR01536 338 rasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeealel 385
                                             ras+p+yl+s++++++g+k+vLsGeG+DE+fgGY yf++a+++++l+ 
  lcl|FitnessBrowser__Koxy:BWI76_RS08180 325 RASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHKAPNAKELHE 372
                                             ********************************************9984 PP

  == domain 2  score: 79.1 bits;  conditional E-value: 1.9e-26
                               TIGR01536 436 leellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr..dgkeKvlLreaaeel 504
                                              ee++r+  +l++ d+ ra+ ++++a+++E+RvPflDk+++++a++i+p+ k+    ++eK++Lre++e++
  lcl|FitnessBrowser__Koxy:BWI76_RS08180 371 HEETVRKLQALHMFDCARAN-KAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCgnGKMEKHVLRECFESY 440
                                             57889999999*********.****************************8888666889************ PP

                               TIGR01536 505 lPeeileRkKeaf 517
                                             lP ++++R+Ke+f
  lcl|FitnessBrowser__Koxy:BWI76_RS08180 441 LPASVAWRQKEQF 453
                                             ***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (553 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: 5.40
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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