Alignments for a candidate for dapC in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Paraburkholderia bryophila 376MFSha3.1

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate H281DRAFT_00600 H281DRAFT_00600 succinyldiaminopimelate aminotransferase apoenzyme

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



>FitnessBrowser__Burk376:H281DRAFT_00600
          Length = 405

 Score =  469 bits (1208), Expect = e-137
 Identities = 241/403 (59%), Positives = 291/403 (72%), Gaps = 11/403 (2%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           +NP LD+L PYPFEKLRAL  D   P    P I+  IGEPKH  P  +  A+ A+L GLS
Sbjct: 1   VNPLLDSLQPYPFEKLRALFKDVA-PAAGFPHISFGIGEPKHPTPTLITDAVIASLGGLS 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSAGA-- 118
            YP+T G   LR++I++W+++RY +P  DP ++VLPV GSREALFA AQTVIDP   A  
Sbjct: 60  AYPATVGSLPLRESIAKWVTQRYGLPPVDPATQVLPVSGSREALFALAQTVIDPRRNAKG 119

Query: 119 ---LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSP 175
              +V+CPNPFYQIYEGAA+LAGA PY+VN+DPAR+F      VP +VW RTQL++VCSP
Sbjct: 120 EPAIVLCPNPFYQIYEGAAILAGAEPYFVNSDPARNFACDYSAVPADVWARTQLLYVCSP 179

Query: 176 GNPAGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYT 235
           GNP G V++LE+WR LF LSDRHGFVIA+ ECYSEIY DE   PLG L+AA +LGR  Y 
Sbjct: 180 GNPTGAVLTLEDWRELFALSDRHGFVIASDECYSEIYFDEANAPLGGLEAAHKLGRG-YD 238

Query: 236 NLVAFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRM 295
            L+  SSLSKRSNVPGMRSGFVAGDAA+L  FLLYRTYHG+A+S V  +ASIAAW+    
Sbjct: 239 RLIMLSSLSKRSNVPGMRSGFVAGDAAILKDFLLYRTYHGAALSTVFQSASIAAWNDEAH 298

Query: 296 CRKT-AQYRAKFEAVLPILQNVLDVRAPQASFYLWAG---TPGSDTAFARELYGRTGVTV 351
            R+  A+Y  KF  V P+L  VLDVR P A+FYLWA    T  +DT FA+ LY    VTV
Sbjct: 299 VRENRAKYVQKFSTVTPMLAAVLDVRLPDAAFYLWADVSRTGLTDTEFAQRLYADYNVTV 358

Query: 352 LPGSLLAREAHNANPGQGRIRIALVAPLDQCVQAAERIAHFAR 394
           LPGS LAR AH  NPG+  +R+ALVA +D+C Q A+RI  F R
Sbjct: 359 LPGSFLARTAHGVNPGRNFVRLALVADVDECTQGAQRIVDFCR 401


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: 553
Number of extensions: 19
Number of successful extensions: 6
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: 405
Length adjustment: 31
Effective length of query: 366
Effective length of database: 374
Effective search space:   136884
Effective search space used:   136884
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 H281DRAFT_00600 H281DRAFT_00600 (succinyldiaminopimelate aminotransferase apoenzyme)
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.18188.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.8e-186  605.7   0.0     2e-186  605.5   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00600  H281DRAFT_00600 succinyldiaminop


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00600  H281DRAFT_00600 succinyldiaminopimelate aminotransferase apoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  605.5   0.0    2e-186    2e-186       1     395 []       1     400 [.       1     400 [. 0.98

  Alignments for each domain:
  == domain 1  score: 605.5 bits;  conditional E-value: 2e-186
                                    TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPttkG 66 
                                                  +np l++l+pyPfekl++l+kdv p+a  ++i++ iGePkh+tP+++++a++++l +ls+yP+t G
  lcl|FitnessBrowser__Burk376:H281DRAFT_00600   1 VNPLLDSLQPYPFEKLRALFKDVAPAAGFPHISFGIGEPKHPTPTLITDAVIASLGGLSAYPATVG 66 
                                                  599*************************************************************** PP

                                    TIGR03538  67 lpelreaiaeWlerrfelpagvdperqvlPvnGtrealfafvqavidrae.....kalvvlPnPfy 127
                                                  +  lre+ia+W+++r+ lp  vdp++qvlPv G+realfa++q+vid+++      a+v++PnPfy
  lcl|FitnessBrowser__Burk376:H281DRAFT_00600  67 SLPLRESIAKWVTQRYGLPP-VDPATQVLPVSGSREALFALAQTVIDPRRnakgePAIVLCPNPFY 131
                                                  ********************.**************************9998888678899****** PP

                                    TIGR03538 128 qiyeGaallagaepyflnctaengfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkklle 193
                                                  qiyeGaa+lagaepyf+n++++ +f  d++avp++vW+r+qll+vcsPgnPtGavl+le++++l++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00600 132 QIYEGAAILAGAEPYFVNSDPARNFACDYSAVPADVWARTQLLYVCSPGNPTGAVLTLEDWRELFA 197
                                                  ****************************************************************** PP

                                    TIGR03538 194 ladkydfiiasdecyselyldeaeaPvGlleaaaelGrddfkrllvfhslskrsnvPGlrsGfvaG 259
                                                  l+d+++f+iasdecyse+y+dea+aP+G leaa++lGr  + rl++++slskrsnvPG+rsGfvaG
  lcl|FitnessBrowser__Burk376:H281DRAFT_00600 198 LSDRHGFVIASDECYSEIYFDEANAPLGGLEAAHKLGR-GYDRLIMLSSLSKRSNVPGMRSGFVAG 262
                                                  *************************************8.8************************** PP

                                    TIGR03538 260 daellkeflryrtyhGcampiavqlasiaaWedekhvrenralyrekfaavleilgavldlelPda 325
                                                  da++lk+fl yrtyhG+a++   q asiaaW+de+hvrenra+y +kf++v+ +l+avld++lPda
  lcl|FitnessBrowser__Burk376:H281DRAFT_00600 263 DAAILKDFLLYRTYHGAALSTVFQSASIAAWNDEAHVRENRAKYVQKFSTVTPMLAAVLDVRLPDA 328
                                                  ****************************************************************** PP

                                    TIGR03538 326 sfylWlkv..pdgddeafaralyeeenvkvlpGrylsreaegvnPGegrvrlalvaeleecveaae 389
                                                  +fylW+ v  +   d++fa++ly++ nv+vlpG++l+r a+gvnPG+++vrlalva+++ec+++a+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00600 329 AFYLWADVsrTGLTDTEFAQRLYADYNVTVLPGSFLARTAHGVNPGRNFVRLALVADVDECTQGAQ 394
                                                  ******99444579**************************************************** PP

                                    TIGR03538 390 rikkll 395
                                                  ri +++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00600 395 RIVDFC 400
                                                  **9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (395 nodes)
Target sequences:                          1  (405 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.26
//
[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