Alignments for a candidate for dapC in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Acidovorax sp. GW101-3H11

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate Ac3H11_2295 N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.17)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2295
          Length = 401

 Score =  466 bits (1198), Expect = e-136
 Identities = 241/401 (60%), Positives = 292/401 (72%), Gaps = 9/401 (2%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MNP L  L PYPFE+LR L A    P     PI+L +GEP+H  P  +  A++ NL GL+
Sbjct: 1   MNPLLSHLQPYPFERLRQLFAGVTPPAA-YSPISLGMGEPRHPTPQFIKDALSNNLEGLA 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSAGA-L 119
            YP+T GEP LR+A ++WL++RY++   DP ++VLPV GSREALFAFAQT+IDPS G  L
Sbjct: 60  SYPATAGEPRLREAFTRWLNQRYALTL-DPGTQVLPVNGSREALFAFAQTIIDPSKGQPL 118

Query: 120 VVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNPA 179
           VVCPNPFYQIYEGAALLAGA PYY  +DPAR+F +    VP+ VW RTQL+FVCSPGNP 
Sbjct: 119 VVCPNPFYQIYEGAALLAGAQPYYAPSDPARNFAVNWDTVPESVWERTQLLFVCSPGNPT 178

Query: 180 GNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLVA 239
           G VM L EW+ LF LSDR+GFVIA+ ECYSEIY   D PPLG LQAA +LGR  + NL++
Sbjct: 179 GAVMPLCEWQKLFALSDRYGFVIASDECYSEIYF-RDEPPLGGLQAAEKLGRRDFKNLIS 237

Query: 240 FSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAW-SMRRMCRK 298
           F+SLSKRSNVPG+RSGFVAGDAAL+  FLLYRTYHGSAMSP+V AASIAAW   + +   
Sbjct: 238 FTSLSKRSNVPGLRSGFVAGDAALIKSFLLYRTYHGSAMSPIVQAASIAAWGDEQHVVEN 297

Query: 299 TAQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPG----SDTAFARELYGRTGVTVLPG 354
             +YR KF  V P+L  V++V  P A FYLWA  P     +D  FAR L  +  VTVLPG
Sbjct: 298 RTRYRKKFAQVTPLLAGVMEVALPDAGFYLWAKVPDALGMTDAEFARALLAQYNVTVLPG 357

Query: 355 SLLAREAHNANPGQGRIRIALVAPLDQCVQAAERIAHFART 395
           S LAREA  +NPG  R+R+ALVA  ++CV+AA RI  F ++
Sbjct: 358 SYLAREAQGSNPGAQRVRMALVAETEECVEAALRIVQFIQS 398


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: 586
Number of extensions: 26
Number of successful extensions: 8
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 Ac3H11_2295 (N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.17))
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.25404.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   2.1e-190  618.6   0.0   2.4e-190  618.4   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2295  N-succinyl-L,L-diaminopimelate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2295  N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.4   0.0  2.4e-190  2.4e-190       1     395 []       1     396 [.       1     396 [. 0.98

  Alignments for each domain:
  == domain 1  score: 618.4 bits;  conditional E-value: 2.4e-190
                                        TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyP 62 
                                                      mnp l++l+pyPfe+l++l+++vtppa +++i+l +GeP+h+tP+f+++al +nle+l++yP
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2295   1 MNPLLSHLQPYPFERLRQLFAGVTPPAAYSPISLGMGEPRHPTPQFIKDALSNNLEGLASYP 62 
                                                      9************************************************************* PP

                                        TIGR03538  63 ttkGlpelreaiaeWlerrfelpagvdperqvlPvnGtrealfafvqavidrae.kalvvlP 123
                                                      +t+G+p+lrea ++Wl++r++l+   dp +qvlPvnG+realfaf+q++id+++ ++lvv+P
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2295  63 ATAGEPRLREAFTRWLNQRYALTL--DPGTQVLPVNGSREALFAFAQTIIDPSKgQPLVVCP 122
                                                      *********************987..*************************9988******* PP

                                        TIGR03538 124 nPfyqiyeGaallagaepyflnctaengfkpdfdavpeevWkrvqllfvcsPgnPtGavlsl 185
                                                      nPfyqiyeGaallaga+py+ +++++ +f  ++d+vpe+vW+r+qllfvcsPgnPtGav++l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2295 123 NPFYQIYEGAALLAGAQPYYAPSDPARNFAVNWDTVPESVWERTQLLFVCSPGNPTGAVMPL 184
                                                      ************************************************************** PP

                                        TIGR03538 186 eelkklleladkydfiiasdecyselyldeaeaPvGlleaaaelGrddfkrllvfhslskrs 247
                                                       e++kl++l+d+y+f+iasdecyse+y+  +e+P+G l+aa +lGr+dfk+l+ f+slskrs
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2295 185 CEWQKLFALSDRYGFVIASDECYSEIYF-RDEPPLGGLQAAEKLGRRDFKNLISFTSLSKRS 245
                                                      ****************************.556****************************** PP

                                        TIGR03538 248 nvPGlrsGfvaGdaellkeflryrtyhGcampiavqlasiaaWedekhvrenralyrekfaa 309
                                                      nvPGlrsGfvaGda+l+k+fl yrtyhG+am++ vq+asiaaW de+hv enr++yr+kfa+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2295 246 NVPGLRSGFVAGDAALIKSFLLYRTYHGSAMSPIVQAASIAAWGDEQHVVENRTRYRKKFAQ 307
                                                      ************************************************************** PP

                                        TIGR03538 310 vleilgavldlelPdasfylWlkvpd...gddeafaralyeeenvkvlpGrylsreaegvnP 368
                                                      v+ +l+ v+++ lPda+fylW+kvpd     d++faral ++ nv+vlpG+yl+rea+g+nP
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2295 308 VTPLLAGVMEVALPDAGFYLWAKVPDalgMTDAEFARALLAQYNVTVLPGSYLAREAQGSNP 369
                                                      ************************8633368******************************* PP

                                        TIGR03538 369 Gegrvrlalvaeleecveaaerikkll 395
                                                      G++rvr+alvae+eecveaa ri +++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2295 370 GAQRVRMALVAETEECVEAALRIVQFI 396
                                                      ************************996 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.56
//
[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