GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Burkholderia phytofirmans PsJN

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate BPHYT_RS35090 BPHYT_RS35090 diaminopimelate decarboxylase

Query= BRENDA::P00861
         (420 letters)



>FitnessBrowser__BFirm:BPHYT_RS35090
          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.2482454.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 29.89
//
[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:

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:

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