Alignments for a candidate for dapC in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Dechlorosoma suillum PS

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate Dsui_2708 Dsui_2708 succinyldiaminopimelate transaminase

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



>FitnessBrowser__PS:Dsui_2708
          Length = 401

 Score =  465 bits (1197), Expect = e-136
 Identities = 240/397 (60%), Positives = 286/397 (72%), Gaps = 5/397 (1%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MNP L  L PYPFEKLR L      P  D   I LSIGEP+HA P  + +A+ ANL GL+
Sbjct: 1   MNPFLAKLQPYPFEKLRQLFQGV-TPNPDYQEIKLSIGEPQHATPGFIKEALTANLGGLA 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSAG--A 118
            YP+++G PALRQAI+ W+ RRY +   +P++E+LPV GSREALFAFAQTVIDPS G   
Sbjct: 60  NYPTSQGTPALRQAIAAWMERRYGLAGVNPDTEILPVNGSREALFAFAQTVIDPSRGYVP 119

Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178
           LVV PNPFYQIYEGAA LAGA PY++N  P  DF L    + +  W R QL++VCSPGNP
Sbjct: 120 LVVSPNPFYQIYEGAAYLAGAEPYFLNTLPENDFSLELEALSEADWARVQLLYVCSPGNP 179

Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238
            G V+ LE+W+ LF LSD++GFVIA+ ECYSEIY DE  PPLG LQAA++LGR  +  LV
Sbjct: 180 TGKVLDLEDWKKLFALSDKYGFVIASDECYSEIYFDEAKPPLGGLQAAKQLGRG-FERLV 238

Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCRK 298
            FSSLSKRSNVPG+RSGFVAGDAA+L +FLLYRTYHG AM+P V AAS  AW+     R+
Sbjct: 239 MFSSLSKRSNVPGLRSGFVAGDAAVLKKFLLYRTYHGGAMNPAVQAASAIAWNEEAHARE 298

Query: 299 T-AQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLL 357
              QY+ KF+AV PI+ +VL    P ASFYLWA TP +DT FAR L     V VLPGS L
Sbjct: 299 NRRQYKEKFDAVTPIVASVLQTGLPDASFYLWARTPIADTEFARRLLADYNVVVLPGSYL 358

Query: 358 AREAHNANPGQGRIRIALVAPLDQCVQAAERIAHFAR 394
           AREA   NPG+  +RIALVAPL  C++AAERI  F +
Sbjct: 359 AREARGVNPGENFVRIALVAPLADCLEAAERIRLFVQ 395


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: 578
Number of extensions: 25
Number of successful extensions: 5
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: 401
Length adjustment: 31
Effective length of query: 366
Effective length of database: 370
Effective search space:   135420
Effective search space used:   135420
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 Dsui_2708 Dsui_2708 (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.25960.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.6e-190  619.0   0.0   1.8e-190  618.8   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_2708  Dsui_2708 succinyldiaminopimelat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2708  Dsui_2708 succinyldiaminopimelate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.8   0.0  1.8e-190  1.8e-190       1     395 []       1     394 [.       1     394 [. 0.99

  Alignments for each domain:
  == domain 1  score: 618.8 bits;  conditional E-value: 1.8e-190
                         TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPttkGlpelreaiaeW 77 
                                       mnp l++l+pyPfekl++l+++vtp+ d++ei+lsiGeP+hatP f++eal++nl +l++yPt++G+p+lr+aia+W
  lcl|FitnessBrowser__PS:Dsui_2708   1 MNPFLAKLQPYPFEKLRQLFQGVTPNPDYQEIKLSIGEPQHATPGFIKEALTANLGGLANYPTSQGTPALRQAIAAW 77 
                                       9**************************************************************************** PP

                         TIGR03538  78 lerrfelpagvdperqvlPvnGtrealfafvqavidrae..kalvvlPnPfyqiyeGaallagaepyflnctaengf 152
                                       +err+ l+  v+p++++lPvnG+realfaf+q+vid+++   +lvv+PnPfyqiyeGaa+lagaepyfln+ +en+f
  lcl|FitnessBrowser__PS:Dsui_2708  78 MERRYGLAG-VNPDTEILPVNGSREALFAFAQTVIDPSRgyVPLVVSPNPFYQIYEGAAYLAGAEPYFLNTLPENDF 153
                                       ******986.***************************99889*********************************** PP

                         TIGR03538 153 kpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkklleladkydfiiasdecyselyldeaeaPvGlleaaael 229
                                         +++a++e  W+rvqll+vcsPgnPtG+vl+le++kkl++l+dky+f+iasdecyse+y+dea++P+G l+aa++l
  lcl|FitnessBrowser__PS:Dsui_2708 154 SLELEALSEADWARVQLLYVCSPGNPTGKVLDLEDWKKLFALSDKYGFVIASDECYSEIYFDEAKPPLGGLQAAKQL 230
                                       ***************************************************************************** PP

                         TIGR03538 230 GrddfkrllvfhslskrsnvPGlrsGfvaGdaellkeflryrtyhGcampiavqlasiaaWedekhvrenralyrek 306
                                       Gr  f+rl++f+slskrsnvPGlrsGfvaGda++lk+fl yrtyhG am++avq+as  aW++e+h renr++y+ek
  lcl|FitnessBrowser__PS:Dsui_2708 231 GR-GFERLVMFSSLSKRSNVPGLRSGFVAGDAAVLKKFLLYRTYHGGAMNPAVQAASAIAWNEEAHARENRRQYKEK 306
                                       *8.9************************************************************************* PP

                         TIGR03538 307 faavleilgavldlelPdasfylWlkvpdgddeafaralyeeenvkvlpGrylsreaegvnPGegrvrlalvaelee 383
                                       f+av+ i+++vl+  lPdasfylW+++ ++ d++far+l ++ nv vlpG+yl+rea gvnPGe++vr+alva+l++
  lcl|FitnessBrowser__PS:Dsui_2708 307 FDAVTPIVASVLQTGLPDASFYLWART-PIADTEFARRLLADYNVVVLPGSYLAREARGVNPGENFVRIALVAPLAD 382
                                       ***************************.5************************************************ PP

                         TIGR03538 384 cveaaerikkll 395
                                       c eaaeri+ ++
  lcl|FitnessBrowser__PS:Dsui_2708 383 CLEAAERIRLFV 394
                                       ********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (395 nodes)
Target sequences:                          1  (401 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.66
//
[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