GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysA in Burkholderia phytofirmans PsJN

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate BPHYT_RS35090 BPHYT_RS35090 diaminopimelate decarboxylase

Query= SwissProt::E0IWI3
         (420 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS35090 BPHYT_RS35090
           diaminopimelate decarboxylase
          Length = 413

 Score =  532 bits (1371), Expect = e-156
 Identities = 254/405 (62%), Positives = 323/405 (79%), Gaps = 2/405 (0%)

Query: 15  ENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIHILRLMREQGVKVDS 74
           + L+ L  E G P+WVYDA  IRR+IA L+ FDV+R+AQKACSN+HIL+LMR++G  VD+
Sbjct: 6   QQLVELAHEHGTPLWVYDADTIRRRIAELRSFDVIRYAQKACSNLHILKLMRDEGAMVDA 65

Query: 75  VSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVS 134
           VSLGEI+R+LAAG+ P   P+ +VFTAD+ID ATL  V E +I VNAGS+DML+Q+G+ +
Sbjct: 66  VSLGEIKRSLAAGFKPDGDPEGVVFTADLIDHATLATVIEHRITVNAGSLDMLEQIGRHA 125

Query: 135 P-GHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIG 193
           P GHRVWLR+NPGFGHGHS KTNTGGE+SKHGIW  D+P A+++++R+ L+LVG+HMHIG
Sbjct: 126 PEGHRVWLRINPGFGHGHSNKTNTGGEHSKHGIWLDDVPRAVELVRRYRLKLVGLHMHIG 185

Query: 194 SGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAARE 253
           SGVDY HL +VC AMV  V   G D++AISAGGGLSVPY++GE  +D  HY+ LW+AAR 
Sbjct: 186 SGVDYGHLSRVCEAMVEAVKGLGHDIEAISAGGGLSVPYREGEPDIDVAHYFRLWDAARR 245

Query: 254 QIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDAGFNDLMRPAMYGS 313
           QI  H+GH V+LEIEPGRFLVAQSGVL+ +V ++ +  ++ F L+DAGFNDL+RP+ YGS
Sbjct: 246 QIETHVGHRVRLEIEPGRFLVAQSGVLVAEVHALNRRPAQQFALLDAGFNDLVRPSFYGS 305

Query: 314 YHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRALPEVKAGDYLVLH 373
           +H ++ L  DG +L  AP     VAGPLCE+GDVFTQ E G +  R++   + GD++V H
Sbjct: 306 HHEMTVLRRDG-ALSEAPIDSFAVAGPLCEAGDVFTQAESGVITNRSIHTPEVGDFIVFH 364

Query: 374 DTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALE 418
           D GAYGASMSSNYNSRPL PEVL D+G+ RLIRRRQTI+ELLALE
Sbjct: 365 DAGAYGASMSSNYNSRPLAPEVLLDHGKPRLIRRRQTIDELLALE 409


Lambda     K      H
   0.320    0.136    0.405 

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: 621
Number of extensions: 33
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: 420
Length of database: 413
Length adjustment: 31
Effective length of query: 389
Effective length of database: 382
Effective search space:   148598
Effective search space used:   148598
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate BPHYT_RS35090 BPHYT_RS35090 (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.18371.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.6e-122  394.2   0.0   3.2e-122  393.9   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS35090  BPHYT_RS35090 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS35090  BPHYT_RS35090 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.9   0.0  3.2e-122  3.2e-122      15     416 ..       7     409 ..       2     410 .. 0.95

  Alignments for each domain:
  == domain 1  score: 393.9 bits;  conditional E-value: 3.2e-122
                                TIGR01048  15 dlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgGEl 84 
                                              +l ela+e+gtPl+vyd++t+r+r+++l++++     ++ YA+KA+snl++l+l+++eG+ +d+vs GE+
  lcl|FitnessBrowser__BFirm:BPHYT_RS35090   7 QLVELAHEHGTPLWVYDADTIRRRIAELRSFD-----VIRYAQKACSNLHILKLMRDEGAMVDAVSLGEI 71 
                                              7899************************9887.....79******************************* PP

                                TIGR01048  85 eralaAgvk....aekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnp 150
                                              +r laAg+k    +e +vf+++ +++++l++++e++i+ +n++s+++le++ + a+e     rv+lR+np
  lcl|FitnessBrowser__BFirm:BPHYT_RS35090  72 KRSLAAGFKpdgdPEGVVFTADLIDHATLATVIEHRIT-VNAGSLDMLEQIGRHAPEG---HRVWLRINP 137
                                              ********9889899**********************8.******************9...9******** PP

                                TIGR01048 151 dvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklle 220
                                              ++++ ++++++TG ++sK+Gi++++  +a+el+ + + l+lvG+h+HIGS++++ +  + + ++v ++  
  lcl|FitnessBrowser__BFirm:BPHYT_RS35090 138 GFGHGHSNKTNTGGEHSKHGIWLDDVPRAVELVRRYR-LKLVGLHMHIGSGVDYGHLSRVCEAMV-EA-- 203
                                              ************************9999998887766.**************9988766665544.44.. PP

                                TIGR01048 221 elkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekea.elglklklilEpGRslvanagvl 289
                                               +k  g ++e++++GGGl+++y+e e  +d+++y + + ++ ++   ++g++++l +EpGR+lva++gvl
  lcl|FitnessBrowser__BFirm:BPHYT_RS35090 204 -VKGLGHDIEAISAGGGLSVPYREGEPDIDVAHYFRLWDAARRQIEtHVGHRVRLEIEPGRFLVAQSGVL 272
                                              .4446**************************************9999*********************** PP

                                TIGR01048 290 ltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkr...leeeetetvdvvGplCEsgDvlakd 356
                                              +++V+++ +++ ++f+l Dag+ndl+Rp+ Y++ he+++l+r   l+e++   + v+GplCE+gDv+++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS35090 273 VAEVHALNRRPAQQFALLDAGFNDLVRPSFYGSHHEMTVLRRdgaLSEAPIDSFAVAGPLCEAGDVFTQA 342
                                              ****************************************98887889999999***************9 PP

                                TIGR01048 357 .......relpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                                     r++ + e Gd+++ ++aGAYgasmssnYnsrp + evl+++gk rlirrr+t+++llale
  lcl|FitnessBrowser__BFirm:BPHYT_RS35090 343 esgvitnRSIHTPEVGDFIVFHDAGAYGASMSSNYNSRPLAPEVLLDHGKPRLIRRRQTIDELLALE 409
                                              9999999*********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (413 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.94
//
[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