Alignments for a candidate for asnB in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Acidovorax sp. GW101-3H11

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate Ac3H11_1552 Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4)

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1552
          Length = 584

 Score =  231 bits (588), Expect = 9e-65
 Identities = 178/625 (28%), Positives = 295/625 (47%), Gaps = 67/625 (10%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  GV N    A    ++++ K ++  I +RG D  G         G  RL+++D EN
Sbjct: 1   MCGIAGVVN----AAGVTKDDVWKMID-CIKYRGVDEQGVEDLGGAVLGHARLAVVDPEN 55

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QP+S  D   W++FNGEI+N+IELRE+L+AKGY F +  DTEVL+  +    E+    
Sbjct: 56  GMQPMSSTDGKVWVVFNGEIFNFIELREQLKAKGYKFKSRCDTEVLVHLWCEKGEKMLDD 115

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLM-VAQNDIEIDKE 179
           L GMFAF IW++       ARD  GIKP +Y      V FASE K+++ + + + ++++ 
Sbjct: 116 LVGMFAFFIWDQRTQTGMLARDRQGIKPCFYAPYQGGVAFASEMKAILALPKFERKVNES 175

Query: 180 ALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANF-KPVQTEE---- 234
           AL    +F + P P T    ++ + PG           TF  Y   +F +PV+  E    
Sbjct: 176 ALGNVFTFNYCPPPETCFEGIRHLMPG-----------TFIRYGGGSFSEPVRYWEWPLD 224

Query: 235 -DKLVKEVRD---AIYDSVNVHMRSDVPVGSFLSGGIDSSFIVS--VAKEFHPSLKTFSV 288
            ++L  E  D   A+ ++V + MR DV  G FLSGG+DSS I +  V +   P L    +
Sbjct: 225 GERLDAEQADLERALDEAVKLQMRFDVDGGLFLSGGVDSSVIANRLVPQWNRPRLDAIGL 284

Query: 289 GFEQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFV 348
             E +GFSE   A+  A  L I   +  I P +       +V H + P  D +    Y +
Sbjct: 285 RIEHEGFSEYAYAERVATDLNINLSALDIQPSDIPEIARSVVRHAEQPHGDFSFFLFYLL 344

Query: 349 AKEAKKHVTVAL-SGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGMR 407
           +++A +   + + +G+G DE+  G+                        H      E  R
Sbjct: 345 SRKAHEMGKIVMFTGDGPDEVMLGFR-----------------------HNEQFFSEMTR 381

Query: 408 GKSLLERGCTPLQDRYIGNAKIFEESVKKQLLK-HYNPNLSYRDVTKTYFTESSSYSDIN 466
               +          Y        E  +K+++   + P+         + +    + D+ 
Sbjct: 382 ANFSMR--------SYFDLISYSSEKDRKRMMSVSFLPHT--EGALDKFMSIIEPFRDLE 431

Query: 467 KMQYV---DIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTT 523
            M+ V   ++   M G+  +K D+M    S+E R PFLD  V ++ +++P   K   G  
Sbjct: 432 PMEQVAAYELTALMPGNNSVKGDRMGACWSIEARAPFLDHRVSELLARLPITSKFHQGVG 491

Query: 524 KYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIHKDYVLQ 583
           K+ L+KAAE       + R K    +PI  W+K  + +W R+ +  S    +  ++ +L 
Sbjct: 492 KHFLKKAAENYYDRDFVFRPKTMPTLPIGEWIKGPLYQWARDTLALSDGGRF-DRNELLV 550

Query: 584 LLEDHCADKADNSRKIWTVLIFMIW 608
           +LE+H +   ++++++ TVL+  +W
Sbjct: 551 MLEEHRSGLHNHTKQLRTVLMTKLW 575


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: 840
Number of extensions: 33
Number of successful extensions: 6
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: 584
Length adjustment: 37
Effective length of query: 595
Effective length of database: 547
Effective search space:   325465
Effective search space used:   325465
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 Ac3H11_1552 (Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4))
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.29514.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   7.9e-121  390.5   0.0   9.5e-121  390.2   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1552  Asparagine synthetase [glutamine


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1552  Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.2   0.0  9.5e-121  9.5e-121       1     515 [.       2     513 ..       2     514 .. 0.91

  Alignments for each domain:
  == domain 1  score: 390.2 bits;  conditional E-value: 9.5e-121
                                        TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsega 62 
                                                      Cgiag+v++      +++ + +m++ ++ RG D++gv  + +  +a+lgh+RLa++d ++g+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1552   2 CGIAGVVNAAGV---TKDDVWKMIDCIKYRGVDEQGV--E-DLGGAVLGHARLAVVDPENGM 57 
                                                      ********9554...4578*****************5..4.579****************** PP

                                        TIGR01536  63 QPlsnek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGm 123
                                                      QP+s+++ +v++vfnGEI+N+ eLre+l++kGy+F++++DtEV+++++ e ge+++++L Gm
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1552  58 QPMSSTDgKVWVVFNGEIFNFIELREQLKAKGYKFKSRCDTEVLVHLWCEKGEKMLDDLVGM 119
                                                      ************************************************************** PP

                                        TIGR01536 124 FAfalwdekkgelflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaell 185
                                                      FAf +wd+++++ +laRDr GikP +ya  qg ++faSE+Ka+lal++++++++++al +++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1552 120 FAFFIWDQRTQTGMLARDRQGIKPCFYAPYQGGVAFASEMKAILALPKFERKVNESALGNVF 181
                                                      ************************************************************** PP

                                        TIGR01536 186 tlqlvptektlfkevkelepakal.dgeeklee...ywevekeevkeseeelveelrelled 243
                                                      t+++ p+++t+f+++++l+p+    +g  +++e   ywe   +  +   ++  ++l+++l +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1552 182 TFNYCPPPETCFEGIRHLMPGTFIrYGGGSFSEpvrYWEWPLDGERL--DAEQADLERALDE 241
                                                      **********************99877888887888**998876555..666789******* PP

                                        TIGR01536 244 avkkrlvadvpvgvllSGGlDSslvaaiakkeak.sevktFsigfe.dskdldeskaarkva 303
                                                      avk +++ dv  g++lSGG+DSs++a  +  + +    ++ +ig+  +++ ++e ++a++va
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1552 242 AVKLQMRFDVDGGLFLSGGVDSSVIANRLVPQWNrP--RLDAIGLRiEHEGFSEYAYAERVA 301
                                                      **************************9999998844..5555555555************** PP

                                        TIGR01536 304 delgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaD 365
                                                       +l +++  + i++ ++ +  + v+++ e+p  + + +  ylls++a+e+g  V+++G+G D
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1552 302 TDLNINLSALDIQPSDIPEIARSVVRHAEQPHGDFSFFLFYLLSRKAHEMGKIVMFTGDGPD 363
                                                      ************************************************************** PP

                                        TIGR01536 366 ElfgGYeyfreakaeealelpeaselaekklllqaklakeselkellkakleeelkekeelk 427
                                                      E++ G+   +++ ++e  +    ++++ ++ +   ++ +e++ k++++ ++  +++   +++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1552 364 EVMLGFRHNEQF-FSEMTR----ANFSMRSYFDLISYSSEKDRKRMMSVSFLPHTEGALDKF 420
                                                      *****9766554.444444....234444444445667777778888887777777777777 PP

                                        TIGR01536 428 kelkee....seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsipp 484
                                                       ++ e     + +e++   +l+ l++++  +k Dr+ +++s+E+R+PflD+++ el +++p 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1552 421 MSIIEPfrdlEPMEQVAAYELTALMPGNNSVKgDRMGACWSIEARAPFLDHRVSELLARLPI 482
                                                      6666666667**************************************************** PP

                                        TIGR01536 485 elklrdgkeKvlLreaaeellPeeileRkKe 515
                                                        k+++g  K+ L++aae++  ++ + R+K 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1552 483 TSKFHQGVGKHFLKKAAENYYDRDFVFRPKT 513
                                                      ********************99999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (584 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.30
//
[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