GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysA in Pedobacter sp. GW460-11-11-14-LB5

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate CA265_RS09650 CA265_RS09650 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS09650 CA265_RS09650
           diaminopimelate decarboxylase
          Length = 390

 Score =  256 bits (655), Expect = 6e-73
 Identities = 153/373 (41%), Positives = 214/373 (57%), Gaps = 14/373 (3%)

Query: 8   FQTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCV 67
           F   +TPFY YD D +++      +A    +  I YALKAN N  +L+ +  +  GADCV
Sbjct: 10  FNNIETPFYYYDTDLLQKTLRTCADAAAPYQFHIHYALKANFNSVLLNQIKEIGFGADCV 69

Query: 68  SIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLG 127
           S GE++RA++ G    +IVF+GVGKS  EI +AL L+I   NVES  EL+ +  +A   G
Sbjct: 70  SAGEVRRAVEVGFDHKKIVFAGVGKSDKEINEALDLDIFCFNVESIQELEVLNELAGKKG 129

Query: 128 IKARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIG 187
             A+++IRINPN+DA TH  I+TGL ENKFG+   +  E     K S  L+ + +HFHIG
Sbjct: 130 KTAQVAIRINPNVDAHTHHNITTGLDENKFGINSWDLPECADTLKASPNLKFIGIHFHIG 189

Query: 188 SQLLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEE----TIKLY-DYA 242
           SQ+ +L+       +V + A      G +L+  +VGGG+G+ Y N +      K Y    
Sbjct: 190 SQITNLDVYKNLCVRVNEFAAWFEDKGFNLQVLNVGGGLGIDYHNPDHQIPDFKSYFKIF 249

Query: 243 QGILNALQGLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLY 302
              L    G ++    E GR++V +S  LIT+VLY K  + K FV++DAGM + +RP+LY
Sbjct: 250 SEFLTVKPGQEVHF--ELGRALVGQSASLITRVLYIKNGKKKNFVVLDAGMTELMRPALY 307

Query: 303 HAKHAIRVITPSKGREISP------CDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVG 356
            A H I  ++  K    SP       D+VGP+CES+D F K+   PE   GD  AI   G
Sbjct: 308 QAYHKIENLS-RKSEVGSPESTALKYDIVGPICESTDCFGKEVEQPESFRGDIFAIRSAG 366

Query: 357 AYGSSMASQYNSR 369
           AYG  MAS+YN R
Sbjct: 367 AYGEVMASKYNLR 379


Lambda     K      H
   0.319    0.138    0.389 

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: 367
Number of extensions: 18
Number of successful extensions: 3
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: 405
Length of database: 390
Length adjustment: 31
Effective length of query: 374
Effective length of database: 359
Effective search space:   134266
Effective search space used:   134266
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate CA265_RS09650 CA265_RS09650 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

# 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/TIGR01048.hmm
# target sequence database:        /tmp/gapView.13445.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01048  [M=417]
Accession:   TIGR01048
Description: lysA: diaminopimelate decarboxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.9e-123  398.0   0.0   2.5e-123  397.6   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS09650  CA265_RS09650 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS09650  CA265_RS09650 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.6   0.0  2.5e-123  2.5e-123      22     393 ..      12     385 ..       5     389 .. 0.94

  Alignments for each domain:
  == domain 1  score: 397.6 bits;  conditional E-value: 2.5e-123
                                  TIGR01048  22 efgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgGElerala 89 
                                                +  tP+Y yd++ l++ l++ + a + ++  ++YA+KAn n  +l+ ++e G+g+d+vs GE+ ra++
  lcl|FitnessBrowser__Pedo557:CA265_RS09650  12 NIETPFYYYDTDLLQKTLRTCADAAAPYQFHIHYALKANFNSVLLNQIKEIGFGADCVSAGEVRRAVE 79 
                                                678**********************99988************************************** PP

                                  TIGR01048  90 AgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakth 157
                                                 g++ +kivf+g+gks++e+++al+l+i ++nv+s++ele l+e+a++ gk+a+v++R+np+vda+th
  lcl|FitnessBrowser__Pedo557:CA265_RS09650  80 VGFDHKKIVFAGVGKSDKEINEALDLDIFCFNVESIQELEVLNELAGKKGKTAQVAIRINPNVDAHTH 147
                                                ******************************************************************** PP

                                  TIGR01048 158 eyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkee 225
                                                  i+TGl e+KFGi+  +  e + + +++++l+ +Gih+HIGSqi++l+ +++ + +v ++++ ++++
  lcl|FitnessBrowser__Pedo557:CA265_RS09650 148 HNITTGLDENKFGINSWDLPECADTLKASPNLKFIGIHFHIGSQITNLDVYKNLCVRVNEFAAWFEDK 215
                                                ******************************************************************** PP

                                  TIGR01048 226 gieleeldlGGGlgisyee.eeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltr 292
                                                g++l++l++GGGlgi+y++ +++ pd ++y + + e l+     +  +++ +E GR+lv++++ l+tr
  lcl|FitnessBrowser__Pedo557:CA265_RS09650 216 GFNLQVLNVGGGLGIDYHNpDHQIPDFKSYFKIFSEFLTV----KPGQEVHFELGRALVGQSASLITR 279
                                                *****************87255678888888887766665....57999******************* PP

                                  TIGR01048 293 VesvKevesrkfvlvDagmndliRpalYeayheiaalkr.....leeeetetvdvvGplCEsgDvlak 355
                                                V ++K+ ++++fv+ Dagm++l+RpalY+ayh+i +l+r       e ++ ++d+vGp+CEs D ++k
  lcl|FitnessBrowser__Pedo557:CA265_RS09650 280 VLYIKNGKKKNFVVLDAGMTELMRPALYQAYHKIENLSRksevgSPESTALKYDIVGPICESTDCFGK 347
                                                *************************************9955544445667899*************** PP

                                  TIGR01048 356 drelpeveeGdllavasaGAYgasmssnYnsrprpaev 393
                                                ++e pe  +Gd+ a++saGAYg  m+s+Yn r  ++ v
  lcl|FitnessBrowser__Pedo557:CA265_RS09650 348 EVEQPESFRGDIFAIRSAGAYGEVMASKYNLRDAIRSV 385
                                                *******************************9988777 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (390 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: 10.92
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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