Alignments for a candidate for asnB in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Pseudomonas fluorescens FW300-N2C3

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate AO356_26510 AO356_26510 asparagine synthase

Query= CharProtDB::CH_007942
         (614 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26510
          Length = 631

 Score =  177 bits (449), Expect = 1e-48
 Identities = 158/582 (27%), Positives = 239/582 (41%), Gaps = 78/582 (13%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVL--FGHKRLAVVDIEG 58
           MCG    V    Q      T+D   DTL  RGPD    W     L   G  RLA+V    
Sbjct: 1   MCGFV--VACHHQAPVPTVTLDAALDTLRHRGPDGRASWLSADGLCGIGFHRLAMVGARE 58

Query: 59  GRQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCV 118
             QP    +  D   ++ NGE+Y     R++L A G  F   SD EV+ H Y++   D V
Sbjct: 59  QTQP----FHTDDVHVVVNGEIYQYAAQRQKLEAAGACFATDSDCEVVAHGYLQLGIDYV 114

Query: 119 DHLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVD 178
             LNG FA  +WD +R  LFA RDR GVKP FY          SEIKA++A    + R D
Sbjct: 115 RELNGEFAGVIWDARRRKLFAIRDRWGVKPLFYRLSDQGIHLASEIKALIA-LGAQPRWD 173

Query: 179 RTGLSEIF--GLGPSRTPGTGIFKGIKEIRPAHALTFSKDGLNIWRYWNVESEKHTDSFD 236
              L + F   +GP++T    +F+GI ++ P H L +S  G  +    +   E H  +  
Sbjct: 174 HAALFQHFFASIGPAQT----LFEGIHQVPPGHVLEWSTQGYGVTPLLSAVDEAHDAARQ 229

Query: 237 DTVANVRSL-------FQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPL 289
              +  R          + AV  +   D PV  +LSGG+DS+ + A+AA H    G+  L
Sbjct: 230 HLASAPREWMPRLVDGLRHAVQDRFQGDGPVACYLSGGVDSATVAALAARH----GREGL 285

Query: 290 HTYSIDYEENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVK 349
             +++D+               DD      +  + G  H    +S+  LVDH  +AV   
Sbjct: 286 SAFTVDFGAG-----------TDDATQAAGIAASLGLRHEVVPVSEAQLVDHFADAVRHA 334

Query: 350 DLPGMADVDSSLLWFCREI--KKDFVVSLSGECADEIFGGYPWFH--------------- 392
           +  G   + ++  W    +     +   L+G+ ADE+F GY +                 
Sbjct: 335 ETIGFNTIGAA-RWILGRVLASSGYKAVLAGDGADELFAGYSFSSVERLCARSHNHARLM 393

Query: 393 -----------TADVESGFPWMRSTEER----IKLLSDSWQ-KKLNLKEYVNAKYEETLA 436
                       A++    P      +R    +  L  SW  ++  L+  +  ++ E   
Sbjct: 394 TQVLEGGRQGLAAELGQPLPLFDMDPDRFGGQVPYLLASWNYQRSGLRPLLRTQFLEAFR 453

Query: 437 E---TPLLDGETGVDKA---RRQLFYLNMLWFMTNLLDRKDRMSMGASLEVRVPFADHRL 490
                 +L  +TG   A   RR L       F  ++L   +R  M   +E R PF D+R+
Sbjct: 454 HFNPYEVLMQQTGASAASGLRRSLHLWQKSMFANHIL-VSERFDMAHGIETRYPFLDNRV 512

Query: 491 VEYVWNIPWEMKMHDNREKGILRKALEGILPDDILYRKKSPY 532
                 +P E  +     K  LR+A+  + P+      K P+
Sbjct: 513 TAVAAMLPDEWLVEGAENKRFLREAVAALTPEAARCAAKRPF 554


Lambda     K      H
   0.320    0.137    0.425 

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: 880
Number of extensions: 51
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 614
Length of database: 631
Length adjustment: 37
Effective length of query: 577
Effective length of database: 594
Effective search space:   342738
Effective search space used:   342738
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: 54 (25.4 bits)

Align candidate AO356_26510 AO356_26510 (asparagine synthase)
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.17467.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   3.4e-106  342.2   0.0   4.1e-106  341.9   0.0    1.1  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26510  AO356_26510 asparagine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26510  AO356_26510 asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.9   0.0  4.1e-106  4.1e-106       1     517 []       2     554 ..       2     554 .. 0.85

  Alignments for each domain:
  == domain 1  score: 341.9 bits;  conditional E-value: 4.1e-106
                                       TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQ 63 
                                                     Cg++ +++++a + +   ++++ l+tl+hRGPD+++ w +  +  +++g++RLa++   e++Q
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26510   2 CGFVVACHHQAPVPT--VTLDAALDTLRHRGPDGRASWLS-ADGLCGIGFHRLAMVGAREQTQ 61 
                                                     999999999887666..6899999****************.7999****************** PP

                                       TIGR01536  64 PlsnekevvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAf 126
                                                     P++ ++ v +v+nGEIY + + r++le++G  F t+sD+EV+ + y ++g + v +L+G+FA 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26510  62 PFHTDD-VHVVVNGEIYQYAAQRQKLEAAGACFATDSDCEVVAHGYLQLGIDYVRELNGEFAG 123
                                                     *****9.78****************************************************** PP

                                       TIGR01536 127 alwdekkgelflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlql 189
                                                     ++wd+++++lf+ RDr G+kPL+y   ++ ++ aSEiKal+al  ++++ d++al++ +  ++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26510 124 VIWDARRRKLFAIRDRWGVKPLFYRLSDQGIHLASEIKALIALG-AQPRWDHAALFQHFFASI 185
                                                     ***************************99***************.89**********999995 PP

                                       TIGR01536 190 vptektlfkevkelepakal..........dgeeklee....ywevekeevkeseeelveelr 238
                                                       + +tlf+++++++p+++l               l +     +++++++ ++  +e + +l 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26510 186 -GPAQTLFEGIHQVPPGHVLewstqgygvtP----LLSavdeAHDAARQHLASAPREWMPRLV 243
                                                     .799****************88877754431....21121123445555577778889999** PP

                                       TIGR01536 239 elledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfedskdldeskaark 301
                                                     + l++av+ r  +d pv+++lSGG+DS +vaa+a+++ ++ +  F+++f   +  d++++a+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26510 244 DGLRHAVQDRFQGDGPVACYLSGGVDSATVAALAARHGREGLSAFTVDFG--AGTDDATQAAG 304
                                                     **************************************************..66666779*** PP

                                       TIGR01536 302 vadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGa 364
                                                     +a+ lg++h+ v +se+++++++++ +++ e +  ++  +  ++l +     g+k vL G+Ga
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26510 305 IAASLGLRHEVVPVSEAQLVDHFADAVRHAETIGFNTIGAARWILGRVLASSGYKAVLAGDGA 367
                                                     *************************************************************** PP

                                       TIGR01536 365 DElfgGYeyfreakaeeale........lpeaselaekkl....................... 396
                                                     DElf+GY+        ++ +        +          l                       
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26510 368 DELFAGYSFSSVERLCARSHnharlmtqV----------Leggrqglaaelgqplplfdmdpd 420
                                                     *******9766554444444444443330..........123334455556677777788888 PP

                                       TIGR01536 397 ........llqakla.keselkellkakleeelkekeelkkelkee.....seleellrldle 445
                                                             l  a+++ ++s l+ ll++++ e+ ++++  +  ++++     s l++ l+l  +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26510 421 rfggqvpyL-LASWNyQRSGLRPLLRTQFLEAFRHFNPYEVLMQQTgasaaSGLRRSLHLWQK 482
                                                     888888863.334431444455566666666555554444433333444669999999*9999 PP

                                       TIGR01536 446 lllsdllrakDrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPee 508
                                                      +  + ++++ r  mah++E R+PflD+++  +a+ +p e  ++  ++K+ Lrea+++l Pe+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26510 483 SMFANHILVSERFDMAHGIETRYPFLDNRVTAVAAMLPDEWLVEGAENKRFLREAVAALTPEA 545
                                                     999***********************************************************9 PP

                                       TIGR01536 509 ileRkKeaf 517
                                                      +   K++f
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26510 546 ARCAAKRPF 554
                                                     887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (631 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: 11.01
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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