Alignments for a candidate for asnB in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Marinobacter adhaerens HP15

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate GFF1957 HP15_1914 asparagine synthase, glutamine-hydrolyzing

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__Marino:GFF1957
          Length = 632

 Score =  353 bits (906), Expect = e-101
 Identities = 218/638 (34%), Positives = 348/638 (54%), Gaps = 43/638 (6%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  G      L          ++M Q I HRGPD++G   D+ V    +RLSI+D+ +
Sbjct: 1   MCGIAGFLRTGTLPDREQHHLWAERMGQAIAHRGPDANGVHIDQDVALVHQRLSILDLSS 60

Query: 61  GG-QPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAAS 119
            G QP++     Y I+FNGEIYN+  LRE LE  G++F T +DTEVLLA Y  + E    
Sbjct: 61  AGNQPMASSCGRYIIVFNGEIYNFRSLREGLEQDGFSFKTQTDTEVLLALYARHGESCLR 120

Query: 120 KLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQ-NDIEIDK 178
           +L GMFAF IW+     L+  RD  G KPLYYT  + Q +F SE K+L         +  
Sbjct: 121 QLNGMFAFAIWDAKTKSLFIGRDRLGKKPLYYTDTDGQFFFGSEIKALFATPVVRPALRP 180

Query: 179 EALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTEEDKLV 238
           +A++ +  +Q++P+P T+ A+V K+ PG    +  +G I+ + Y+  +F+PV   E + V
Sbjct: 181 DAIKDFFVYQYIPDPKTIYANVHKLPPGHCMEV-CEGRISVRKYWDLSFRPV---EGRTV 236

Query: 239 KEVRDAIYD----SVNVHMRSDVPVGSFLSGGIDSSFIVS-VAKEFHPSLKTFSVGFEQQ 293
            +++  +YD    +V + M SDVP+G+FLSGGIDSS +V  +A      + T ++GF+ +
Sbjct: 237 SDIKAGLYDVIDEAVRLRMISDVPLGAFLSGGIDSSAVVGLMAGRSSQPVTTCTIGFDDE 296

Query: 294 GFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAK 353
            F E+  A   A     ++    +  E   + L  I   FD+P ADP+ +P +FV++ A+
Sbjct: 297 KFDEIKYADLVARQFKTDHHVFTVK-ETVADNLVGISRFFDEPFADPSFVPTFFVSQLAR 355

Query: 354 KHVTVALSGEGADELFGGYNIYREPL------SLKP---FERIPSGLKKMLLHVAAVMPE 404
             VTVAL+G+G DE F GY+ YR         SL P      +  GL ++  H+    P 
Sbjct: 356 TQVTVALAGDGGDENFAGYSKYRTDAIENRIRSLFPPALRHSLFPGLSRLAGHIPG--PL 413

Query: 405 GMRGKSLLERGCTPLQDRYIG--------NAKIFEESVKKQ---LLKHYNPNLSYRDVTK 453
           G +  SLL    T   D  +G        N ++++  V  +   L   Y+P     D+T+
Sbjct: 414 GKKASSLLG---TVALDPDLGFFTSNCFFNPRVWKRVVSPEFAALTDDYDP----ADITR 466

Query: 454 TYFTESSSYSDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIP 513
            ++ E+ +   ++++ Y DI T++ GDIL+K D+M+MANSLE R P LD  V + A+ IP
Sbjct: 467 HHYQEAPAEDHLSRILYTDIKTYLPGDILVKVDRMSMANSLETRAPLLDYRVVEYAAGIP 526

Query: 514 DELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNII--QESQ 571
             LK K    K++L++    ++ E +L RKK+GF VP+  WL++E+      ++   +S 
Sbjct: 527 SALKLKGNCKKHVLKECFSDLLDEDILYRKKMGFSVPLAQWLRSEIRAIAEPLLTGPDSG 586

Query: 572 TDAYIHKDYVLQLLEDHCADKADNSRKIWTVLIFMIWH 609
              Y   + V  L + H +     ++++W++++F +W+
Sbjct: 587 LSRYFRMEQVRALWQAHLSGDNRFTQELWSMVVFALWY 624


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: 984
Number of extensions: 43
Number of successful extensions: 7
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: 632
Length of database: 632
Length adjustment: 38
Effective length of query: 594
Effective length of database: 594
Effective search space:   352836
Effective search space used:   352836
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 GFF1957 HP15_1914 (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.26688.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.9e-153  496.5   0.0     7e-153  496.2   0.0    1.1  1  lcl|FitnessBrowser__Marino:GFF1957  HP15_1914 asparagine synthase, g


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1957  HP15_1914 asparagine synthase, glutamine-hydrolyzing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.2   0.0    7e-153    7e-153       1     517 []       2     560 ..       2     560 .. 0.89

  Alignments for each domain:
  == domain 1  score: 496.2 bits;  conditional E-value: 7e-153
                           TIGR01536   1 Cgiagivdlkakake..eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.ev 71 
                                         Cgiag++   +  ++  ++  +++m +++ahRGPDa+gv++d   ++++l+h+RL+i dls++ +QP+++   ++
  lcl|FitnessBrowser__Marino:GFF1957   2 CGIAGFLRTGTLPDReqHHLWAERMGQAIAHRGPDANGVHID---QDVALVHQRLSILDLSSAgNQPMASSCgRY 73 
                                         *******9988777654555689*******************...79*************9998*******99** PP

                           TIGR01536  72 vivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGik 146
                                         +ivfnGEIYN+++Lre le++G++F+t++DtEV+La+y  +ge ++ +L+GmFAfa+wd+k++ lf+ RDrlG+k
  lcl|FitnessBrowser__Marino:GFF1957  74 IIVFNGEIYNFRSLREGLEQDGFSFKTQTDTEVLLALYARHGESCLRQLNGMFAFAIWDAKTKSLFIGRDRLGKK 148
                                         *************************************************************************** PP

                           TIGR01536 147 PLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekleey 218
                                         PLYy+ ++g+++f+SEiKal+a++ ++++l+ +a+++++ +q+ p++kt++++v++l+p++++   +g  ++++y
  lcl|FitnessBrowser__Marino:GFF1957 149 PLYYTDTDGQFFFGSEIKALFATPVVRPALRPDAIKDFFVYQYIPDPKTIYANVHKLPPGHCMevcEGRISVRKY 223
                                         ***************************************************************98888889999* PP

                           TIGR01536 219 wevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfedskd 292
                                         w+++ +     ++++ ++ l + + +av+ r+++dvp+g++lSGG+DSs+v+ +++  + ++v+t +igf+ +++
  lcl|FitnessBrowser__Marino:GFF1957 224 WDLSFRPvEGRTVSDIKAGLYDVIDEAVRLRMISDVPLGAFLSGGIDSSAVVGLMAGRSSQPVTTCTIGFD-DEK 297
                                         ****999556678899999****************************************************.9** PP

                           TIGR01536 293 ldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDEl 367
                                         +de k+a  va+++ t+h+ +++ +e+v+++l  + + ++ep+a+++ +p++++s+lar + v+V+L G+G+DE 
  lcl|FitnessBrowser__Marino:GFF1957 298 FDEIKYADLVARQFKTDHHVFTV-KETVADNLVGISRFFDEPFADPSFVPTFFVSQLARTQ-VTVALAGDGGDEN 370
                                         *******************9998.5799*********************************.************* PP

                           TIGR01536 368 fgGYeyfreakaeeale.....................lpeaselaekkl......................... 396
                                         f+GY+++r+   e++++                     +                                    
  lcl|FitnessBrowser__Marino:GFF1957 371 FAGYSKYRTDAIENRIRslfppalrhslfpglsrlaghI----------Pgplgkkassllgtvaldpdlgffts 435
                                         *****************9998888888855544443331..........13333334455777778888888444 PP

                           TIGR01536 397 ..llqaklakeselkellkakleeelke.keelkkelkeeseleellrldlelllsdllrak.DrvsmahslEvR 467
                                           + + ++ k++++ e++  + +++ +  ++++ +e ++e +l+++l+ d++++l++++++k Dr+sma+slE R
  lcl|FitnessBrowser__Marino:GFF1957 436 ncFFNPRVWKRVVSPEFAALTDDYDPADiTRHHYQEAPAEDHLSRILYTDIKTYLPGDILVKvDRMSMANSLETR 510
                                         4433333333334444444333333333133444555666*********************************** PP

                           TIGR01536 468 vPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                         +P+lD ++ve+a+ ip  lkl+ +++K++L+e++ +ll e+il+RkK++f
  lcl|FitnessBrowser__Marino:GFF1957 511 APLLDYRVVEYAAGIPSALKLKGNCKKHVLKECFSDLLDEDILYRKKMGF 560
                                         ************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (632 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: 00:00:00.03
# Mc/sec: 9.01
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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