GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Pseudomonas stutzeri RCH2

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate GFF1433 Psest_1470 succinyldiaminopimelate transaminase

Query= metacyc::MONOMER-6501
         (397 letters)



>FitnessBrowser__psRCH2:GFF1433
          Length = 398

 Score =  428 bits (1100), Expect = e-124
 Identities = 227/398 (57%), Positives = 271/398 (68%), Gaps = 4/398 (1%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MN  L+ LHPYPFEKLR LLA A  PT D   I LSIGEPKH +P  V QA+A NL  L+
Sbjct: 1   MNNALNLLHPYPFEKLRGLLAGAEAPT-DKRHIALSIGEPKHRSPDFVAQALADNLDQLA 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAP--DPESEVLPVLGSREALFAFAQTVIDPSAGA 118
           VYP+T G PALR+ I++W  RR+ + A   DP   VLPV G+REALFAF Q V+D     
Sbjct: 60  VYPTTLGIPALRETIARWCERRFGLAADALDPARHVLPVNGTREALFAFTQAVVDRETDG 119

Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178
           LVV PNPFYQIYEGAALLAGATP+Y+       F      VP EVW+R Q++F+CSPGNP
Sbjct: 120 LVVSPNPFYQIYEGAALLAGATPHYLPCLEQNGFNPDFAAVPAEVWQRCQILFLCSPGNP 179

Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238
            G ++ LE  + L  L+D++ FVIAA ECYSE+Y DE  PP G L A   LGR+ Y   V
Sbjct: 180 TGALVPLETLKKLIALADQYDFVIAADECYSELYFDEANPPAGLLTACAALGRNDYKRCV 239

Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCRK 298
            F SLSKRSN+PG+RSGFVAGDA +L  FLLYRTYHG AM      ASIAAW+     R 
Sbjct: 240 VFHSLSKRSNLPGLRSGFVAGDAEILKAFLLYRTYHGCAMPVQTQLASIAAWNDEIHVRA 299

Query: 299 TAQ-YRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLL 357
             + YRAKF+AVL IL  V+DV+ P   FYLW  TP  D  F  EL+ R  VTV+PGS L
Sbjct: 300 NRELYRAKFDAVLEILAPVMDVQRPDGGFYLWPKTPMDDQQFTCELFAREHVTVVPGSYL 359

Query: 358 AREAHNANPGQGRIRIALVAPLDQCVQAAERIAHFART 395
           +RE   A+PG GR+R+ALVAPL +C++AA+RI HF  T
Sbjct: 360 SREVDGASPGAGRVRMALVAPLAECIEAAQRIRHFIET 397


Lambda     K      H
   0.321    0.135    0.412 

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: 508
Number of extensions: 20
Number of successful extensions: 4
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: 397
Length of database: 398
Length adjustment: 31
Effective length of query: 366
Effective length of database: 367
Effective search space:   134322
Effective search space used:   134322
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate GFF1433 Psest_1470 (succinyldiaminopimelate transaminase)
to HMM TIGR03538 (dapC: succinyldiaminopimelate transaminase (EC 2.6.1.17))

# 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/TIGR03538.hmm
# target sequence database:        /tmp/gapView.14902.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03538  [M=395]
Accession:   TIGR03538
Description: DapC_gpp: succinyldiaminopimelate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.6e-208  677.1   0.0     4e-208  677.0   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1433  Psest_1470 succinyldiaminopimela


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1433  Psest_1470 succinyldiaminopimelate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  677.0   0.0    4e-208    4e-208       1     395 []       1     395 [.       1     395 [. 1.00

  Alignments for each domain:
  == domain 1  score: 677.0 bits;  conditional E-value: 4e-208
                           TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPttkGlpelreaia 75 
                                         mn++l+ l+pyPfekl+ ll+++ +p+d+++ialsiGePkh++P+fv++al++nl++l+ yPtt G+p+lre+ia
  lcl|FitnessBrowser__psRCH2:GFF1433   1 MNNALNLLHPYPFEKLRGLLAGAEAPTDKRHIALSIGEPKHRSPDFVAQALADNLDQLAVYPTTLGIPALRETIA 75 
                                         9************************************************************************** PP

                           TIGR03538  76 eWlerrfelpag.vdperqvlPvnGtrealfafvqavidraekalvvlPnPfyqiyeGaallagaepyflnctae 149
                                         +W+errf l+a  +dp+r+vlPvnGtrealfaf+qav+dr+++ lvv+PnPfyqiyeGaallaga+p++l+c ++
  lcl|FitnessBrowser__psRCH2:GFF1433  76 RWCERRFGLAADaLDPARHVLPVNGTREALFAFTQAVVDRETDGLVVSPNPFYQIYEGAALLAGATPHYLPCLEQ 150
                                         *********9999************************************************************** PP

                           TIGR03538 150 ngfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkklleladkydfiiasdecyselyldeaeaPvGlle 224
                                         ngf+pdf avp+evW+r+q+lf+csPgnPtGa+++le+lkkl++lad+ydf+ia+decysely+dea++P+Gll 
  lcl|FitnessBrowser__psRCH2:GFF1433 151 NGFNPDFAAVPAEVWQRCQILFLCSPGNPTGALVPLETLKKLIALADQYDFVIAADECYSELYFDEANPPAGLLT 225
                                         *************************************************************************** PP

                           TIGR03538 225 aaaelGrddfkrllvfhslskrsnvPGlrsGfvaGdaellkeflryrtyhGcampiavqlasiaaWedekhvren 299
                                         a+a+lGr+d+kr++vfhslskrsn+PGlrsGfvaGdae+lk+fl yrtyhGcamp+++qlasiaaW+de hvr+n
  lcl|FitnessBrowser__psRCH2:GFF1433 226 ACAALGRNDYKRCVVFHSLSKRSNLPGLRSGFVAGDAEILKAFLLYRTYHGCAMPVQTQLASIAAWNDEIHVRAN 300
                                         *************************************************************************** PP

                           TIGR03538 300 ralyrekfaavleilgavldlelPdasfylWlkvpdgddeafaralyeeenvkvlpGrylsreaegvnPGegrvr 374
                                         r+lyr+kf+avleil++v+d+++Pd++fylW+k+ + dd++f+ +l+++e+v+v+pG+ylsre++g+ PG+grvr
  lcl|FitnessBrowser__psRCH2:GFF1433 301 RELYRAKFDAVLEILAPVMDVQRPDGGFYLWPKT-PMDDQQFTCELFAREHVTVVPGSYLSREVDGASPGAGRVR 374
                                         **********************************.5*************************************** PP

                           TIGR03538 375 lalvaeleecveaaerikkll 395
                                         +alva+l+ec+eaa+ri++++
  lcl|FitnessBrowser__psRCH2:GFF1433 375 MALVAPLAECIEAAQRIRHFI 395
                                         ******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (395 nodes)
Target sequences:                          1  (398 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.43
//
[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:

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:

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:

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:

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