Alignments for a candidate for asnB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Pedobacter sp. GW460-11-11-14-LB5

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate CA265_RS01810 CA265_RS01810 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__Pedo557:CA265_RS01810
          Length = 595

 Score =  234 bits (598), Expect = 6e-66
 Identities = 170/563 (30%), Positives = 270/563 (47%), Gaps = 18/563 (3%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGF--GFRRLSIIDV 58
           MC   G+ N     +  +Q+  +K M   + H GPD  G +  E      G RRL+I+D+
Sbjct: 1   MCRIAGIINSKNSFEKVNQQ--VKAMCDSMQHGGPDDHGIYTAEKTPLCLGNRRLAILDL 58

Query: 59  ENGG-QPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEA 117
            + G QP+    E   I +NGEIYNY ++R EL   GY F T +DTEV+L  Y+H+ E A
Sbjct: 59  SSTGHQPMLSHKEDLVITYNGEIYNYKQIRTELINLGYIFKTQTDTEVILYAYQHWGETA 118

Query: 118 ASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIEID 177
             KL G+FAF I++K +  +Y  RD  GIKPLYY   N+ + FASE K+   A  D E D
Sbjct: 119 FEKLDGIFAFCIFDKREQCVYLVRDQNGIKPLYYHFANETLTFASEVKAFKHANIDQEND 178

Query: 178 KEALQQYMSFQFVPEPSTLDAHVKKVEPGS--QFTIRPDGDITFKTYFKANFKPVQTEED 235
              +  Y++F  +PEP T   +V  +  GS  ++ IR       ++Y +         E 
Sbjct: 179 NWRI-YYLAFGHIPEPYTTLKNVCSLGKGSFLKYNIR-SAQHLIQSYHEFESTSYIHNES 236

Query: 236 KLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEF-HPSLKTFSVGFEQQG 294
             ++ +R+ +  S+   M SDV +G   SGG+DSS I  +A ++ +  L + S  F +  
Sbjct: 237 YAIERIREQLGHSIKQQMISDVDIGVLFSGGLDSSIITILANQYNNKQLSSISANFNEID 296

Query: 295 FSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKK 354
           FSE          + ++ I ++I+  +++     ++   D P  D   I  +FV K AK 
Sbjct: 297 FSEKKQRNSLLQKINLQKIEQLITYRDFVQNFETVLADMDQPTND--GINTWFVCKTAKA 354

Query: 355 H-VTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGMRGKSLLE 413
           + + V LSG GADELFGGY  +     ++      + L K  L  +       + K L  
Sbjct: 355 NGIKVVLSGLGADELFGGYPSFDRIHKIQNL----NWLSKSALR-STRFSNNTKFKRLYY 409

Query: 414 RGCTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSDINKMQYVDI 473
                    Y+    ++   V  +LL      +                S+  +  + + 
Sbjct: 410 LSLNSPIGEYLCLRGVYSPDVIAELLDIDMKTVIDCLEDIPLHPGIKKTSNETRASWFEF 469

Query: 474 HTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYLLRKAAEG 533
           + +M+  +L   D M+M++ +E+RVPFLD+   D+   I  E+K      K LL +A + 
Sbjct: 470 NMYMQNQLLKDTDFMSMSHGVEVRVPFLDRNFVDLVLSISTEIKFSYEQKKKLLVEAYKE 529

Query: 534 IVPEHVLNRKKLGFPVPIRHWLK 556
            +P     R K+GF  P + W++
Sbjct: 530 DLPVETWKRSKMGFTFPFQEWMR 552


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: 879
Number of extensions: 49
Number of successful extensions: 5
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: 595
Length adjustment: 37
Effective length of query: 595
Effective length of database: 558
Effective search space:   332010
Effective search space used:   332010
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: 53 (25.0 bits)

Align candidate CA265_RS01810 CA265_RS01810 (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.22142.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.9e-130  422.2   0.1   2.2e-130  422.0   0.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS01810  CA265_RS01810 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS01810  CA265_RS01810 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.0   0.1  2.2e-130  2.2e-130       1     517 []       2     543 ..       2     543 .. 0.90

  Alignments for each domain:
  == domain 1  score: 422.0 bits;  conditional E-value: 2.2e-130
                                  TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsn 67 
                                                C iagi+++k+  ++ ++++k+m + ++h GPD++g++   +++  +lg rRLai dls+  +QP+ +
  lcl|FitnessBrowser__Pedo557:CA265_RS01810   2 CRIAGIINSKNSFEKVNQQVKAMCDSMQHGGPDDHGIYTA-EKTPLCLGNRRLAILDLSSTgHQPMLS 68 
                                                99***********9988**********************9.79***************9988*****9 PP

                                  TIGR01536  68 ek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkg 134
                                                +k   vi++nGEIYN++++r el++ Gy F+t++DtEViL ay++wge+++e+L+G FAf ++d++++
  lcl|FitnessBrowser__Pedo557:CA265_RS01810  69 HKeDLVITYNGEIYNYKQIRTELINLGYIFKTQTDTEVILYAYQHWGETAFEKLDGIFAFCIFDKREQ 136
                                                99999*************************************************************** PP

                                  TIGR01536 135 elflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevke 202
                                                 ++l+RD+ GikPLYy   +++l faSE+Ka+ +++ i++e d+   + +l++   p++ t  k+v  
  lcl|FitnessBrowser__Pedo557:CA265_RS01810 137 CVYLVRDQNGIKPLYYHFANETLTFASEVKAFKHAN-IDQENDN-WRIYYLAFGHIPEPYTTLKNVCS 202
                                                *******************************97776.7777655.556677788779*********** PP

                                  TIGR01536 203 lepakal.....dgeekleeywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDS 265
                                                l +++ l     + ++ +++y+e e+++  ++e++++e++re l +++k+++++dv +gvl+SGGlDS
  lcl|FitnessBrowser__Pedo557:CA265_RS01810 203 LGKGSFLkynirSAQHLIQSYHEFESTSYIHNESYAIERIREQLGHSIKQQMISDVDIGVLFSGGLDS 270
                                                ****9998888666777777************************************************ PP

                                  TIGR01536 266 slvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilalee 333
                                                s+++ +a+++ ++++ + s +f+ + d++e+k+ + + +++ ++  e li+  ++++++e v+  +++
  lcl|FitnessBrowser__Pedo557:CA265_RS01810 271 SIITILANQYNNKQLSSISANFN-EIDFSEKKQRNSLLQKINLQKIEQLITYRDFVQNFETVLADMDQ 337
                                                ***********************.******************************************** PP

                                  TIGR01536 334 ptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeealelpease..laekkl... 396
                                                pt+  + i +++++k a+++g+kVvLsG GaDElfgGY  f++ ++ ++l+  ++s+  l+++++   
  lcl|FitnessBrowser__Pedo557:CA265_RS01810 338 PTN--DGINTWFVCKTAKANGIKVVLSGLGADELFGGYPSFDRIHKIQNLN--WLSKsaLRSTRFsnn 401
                                                **5..56889*********************************99999998..333322222222444 PP

                                  TIGR01536 397 ..................llqaklakeselkellkakleeelkekeel..kkelkeeseleellrldl 444
                                                                  l  + + +  + +ell  ++++ +   e+   +  +k++s+  ++   ++
  lcl|FitnessBrowser__Pedo557:CA265_RS01810 402 tkfkrlyylslnspigeyLCLRGVYSPDVIAELLDIDMKTVIDCLEDIplHPGIKKTSNETRASWFEF 469
                                                556777888888887777666667777777777777777766655544003445555888899999** PP

                                  TIGR01536 445 elllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeile 511
                                                + ++++ l+ + D +sm h++EvRvPflD+++v+l+lsi +e+k++ +++K lL ea +e lP e  +
  lcl|FitnessBrowser__Pedo557:CA265_RS01810 470 NMYMQNQLLKDtDFMSMSHGVEVRVPFLDRNFVDLVLSISTEIKFSYEQKKKLLVEAYKEDLPVETWK 537
                                                ******************************************************************** PP

                                  TIGR01536 512 RkKeaf 517
                                                R+K++f
  lcl|FitnessBrowser__Pedo557:CA265_RS01810 538 RSKMGF 543
                                                ****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (595 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 13.25
//
[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