Alignments for a candidate for asnB in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Pseudomonas stutzeri RCH2

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate GFF2874 Psest_2930 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__psRCH2:GFF2874
          Length = 627

 Score =  259 bits (662), Expect = 2e-73
 Identities = 193/627 (30%), Positives = 307/627 (48%), Gaps = 58/627 (9%)

Query: 1   MCGFVGV--FNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDV 58
           MCG  G   F+  P    A     ++++ Q +  RGPD+ G+     +  G RRL I+D+
Sbjct: 38  MCGIAGELRFDNRPADLAA-----VERITQHLTARGPDACGFHSQGPLALGHRRLKIMDL 92

Query: 59  -ENGGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEA 117
            E  GQP+        ++FNG IYNY ELR ELE  GY F ++ DTEVLL  +  + E  
Sbjct: 93  CEASGQPMIDSALGLSMVFNGAIYNYPELRAELEGLGYRFFSEGDTEVLLKGFHAWGEAL 152

Query: 118 ASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIE-- 175
             +L GMFAF IW ++   L+ ARD  G+KPLY +  + ++ FAS   +L+    DI   
Sbjct: 153 LPRLNGMFAFAIWQRDTQQLFIARDRLGVKPLYLSRTDQRLRFASSLPALLKG-GDIAGV 211

Query: 176 IDKEALQQYMSFQ-FVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTEE 234
           ++  AL  YMSF   VP P TL A ++K+ P S   +  +G  T + +++  F   + E 
Sbjct: 212 LNPVALNHYMSFHAVVPAPDTLIAGIEKLPPASWMRVDANGATTTQRWWELQFGAREEER 271

Query: 235 DKLVKEVR----DAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKE--FHPSLKTFSV 288
           +   ++ +    D + ++V +  R+ V VG  LSGG+DSS +V + +E     +L TFS+
Sbjct: 272 NYSFEDWKQRTLDTMREAVAIRQRAAVDVGVLLSGGVDSSLLVGLLREAGVADNLLTFSI 331

Query: 289 GFEQQGFSEVDVAKET---AAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPL 345
           GFE  G    D  K +   A      +    I  +E + +LP       +P+     I  
Sbjct: 332 GFEDAGGERGDEFKYSDLIAKHYKTRHHQLRIQEKEILEQLPAAFQAMSEPMVSHDCIAF 391

Query: 346 YFVAKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEG 405
           Y +++E  KH  V  SG+GADELF GY+ Y  PL       +      +  ++AA     
Sbjct: 392 YLLSREVAKHCKVVQSGQGADELFAGYHWY--PL-------VDGAEDPVAAYLAA----- 437

Query: 406 MRGKSLLERGCTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSDI 465
            R +S  E                + E+V++Q ++         D  + +F +  + + +
Sbjct: 438 FRDRSYEE----------------YAETVQQQWVQGDFSG----DFVRQHFAQPGADAAV 477

Query: 466 NKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKY 525
           +K   +D    +  D + + D MTMA  LE R PFLD  V +++++IP + K   G  KY
Sbjct: 478 DKALRIDSTVMLVDDPVKRVDNMTMAWGLEARTPFLDYRVAELSARIPAKFKLPEG-GKY 536

Query: 526 LLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIHKDYVLQ-L 584
           +L++AA  ++P  V++R K  FPVP    L+     WVR ++ +   +  ++    L+ L
Sbjct: 537 VLKEAARQVIPAEVIDRPKGYFPVPGLKHLQGATLNWVREMLLDPSQERGLYNPQALEKL 596

Query: 585 LEDHCADKAD-NSRKIWTVLIFMIWHS 610
           L D           K+W +    +W S
Sbjct: 597 LADPDGQLTPLRGSKLWQLAAVNLWLS 623


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: 920
Number of extensions: 44
Number of successful extensions: 8
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: 627
Length adjustment: 38
Effective length of query: 594
Effective length of database: 589
Effective search space:   349866
Effective search space used:   349866
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: 54 (25.4 bits)

Align candidate GFF2874 Psest_2930 (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.14110.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.2e-124  403.0   0.0   1.4e-124  402.8   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2874  Psest_2930 asparagine synthase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2874  Psest_2930 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.8   0.0  1.4e-124  1.4e-124       1     516 [.      39     557 ..      39     558 .. 0.89

  Alignments for each domain:
  == domain 1  score: 402.8 bits;  conditional E-value: 1.4e-124
                           TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.evvi 73 
                                         Cgiag +  ++  + + +a++++++ l  RGPDa g++++      +lghrRL i+dl e+  QP+ + +    +
  lcl|FitnessBrowser__psRCH2:GFF2874  39 CGIAGELRFDNRPA-DLAAVERITQHLTARGPDACGFHSQ---GPLALGHRRLKIMDLCEAsGQPMIDSAlGLSM 109
                                         *********88655.579******************7555...9**************9999*********99** PP

                           TIGR01536  74 vfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPL 148
                                         vfnG IYN+ eLr+ele  Gy+F ++ DtEV+L+ +++wge+l+ rL+GmFAfa+w++ +++lf+aRDrlG+kPL
  lcl|FitnessBrowser__psRCH2:GFF2874 110 VFNGAIYNYPELRAELEGLGYRFFSEGDTEVLLKGFHAWGEALLPRLNGMFAFAIWQRDTQQLFIARDRLGVKPL 184
                                         *************************************************************************** PP

                           TIGR01536 149 YyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkelepakal....dgeekleey 218
                                         Y ++++++l faS + all+  +i+  l+  al ++++++ +vp ++tl +++++l+pa+ +    +g+++ +++
  lcl|FitnessBrowser__psRCH2:GFF2874 185 YLSRTDQRLRFASSLPALLKGGDIAGVLNPVALNHYMSFHaVVPAPDTLIAGIEKLPPASWMrvdaNGATTTQRW 259
                                         ****************************************999*****************99898888888888* PP

                           TIGR01536 219 wevekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak.sevktFsigfe 288
                                         we++  +    ++ s+e+ ++++ +++++av+ r +a v vgvllSGG+DSsl++ ++++     ++ tFsigfe
  lcl|FitnessBrowser__psRCH2:GFF2874 260 WELQFGAreeeRNYSFEDWKQRTLDTMREAVAIRQRAAVDVGVLLSGGVDSSLLVGLLREAGVaDNLLTFSIGFE 334
                                         **99876555688899999*************************************9998755589********* PP

                           TIGR01536 289 ..dskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsG 361
                                           + +  de k+   +a++  t+h+++ i+e+e+l++l+  + a+ ep+  +++i  ylls+++ ++ +kVv sG
  lcl|FitnessBrowser__psRCH2:GFF2874 335 daGGERGDEFKYSDLIAKHYKTRHHQLRIQEKEILEQLPAAFQAMSEPMVSHDCIAFYLLSREVAKH-CKVVQSG 408
                                         65567889999********************************************************.******* PP

                           TIGR01536 362 eGaDElfgGYeyfreakaeealelpeaselaekklllqaklakeselkellkakleeelkekeelkkelkeesel 436
                                         +GaDElf+GY+++     +e+   ++++       + ++++++  e+ + +  + + +   +++++++  ++ ++
  lcl|FitnessBrowser__psRCH2:GFF2874 409 QGADELFAGYHWYPLVDGAEDPVAAYLAA------FRDRSYEEYAETVQQQWVQGDFSGDFVRQHFAQPGADAAV 477
                                         **************987766665344333......3344444443333333333333444556667778888889 PP

                           TIGR01536 437 eellrldlelllsdl.lrakDrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeil 510
                                         +++lr d + +l d+ +++ D ++ma++lE+R PflD +++el ++ip++ kl +g  K++L+eaa++++P e+ 
  lcl|FitnessBrowser__psRCH2:GFF2874 478 DKALRIDSTVMLVDDpVKRVDNMTMAWGLEARTPFLDYRVAELSARIPAKFKLPEG-GKYVLKEAARQVIPAEVI 551
                                         99999888877766526777*********************************987.7***************** PP

                           TIGR01536 511 eRkKea 516
                                         +R+K  
  lcl|FitnessBrowser__psRCH2:GFF2874 552 DRPKGY 557
                                         ***965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (627 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: 11.90
//
[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