Alignments for a candidate for lysA in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Pseudomonas putida KT2440

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate PP_2077 PP_2077 diaminopimelate decarboxylase

Query= BRENDA::P00861
         (420 letters)



>FitnessBrowser__Putida:PP_2077
          Length = 410

 Score =  488 bits (1256), Expect = e-142
 Identities = 236/396 (59%), Positives = 300/396 (75%), Gaps = 2/396 (0%)

Query: 23  EFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIHILRLMREQGVKVDSVSLGEIER 82
           + G P+W YD + I  ++  L  FD VRFAQKA  N+H+LRLMR  G+ +D+VSLGE+ER
Sbjct: 14  QHGSPLWAYDTRTIADRVEQLNVFDTVRFAQKANPNLHVLRLMRAHGLVLDAVSLGEMER 73

Query: 83  ALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVSPGHRVWLR 142
           A AAG +    P  +V T D +D+ TLERV   +I VNAGS+DML QLG+ SPGHRVW+R
Sbjct: 74  AFAAGASVDGDPAGVVLTCDALDRPTLERVVASKIEVNAGSIDMLHQLGERSPGHRVWIR 133

Query: 143 VNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGSGVDYAHLE 202
           +NPGFGHGHS+KTNTGGENSKHGIW+ +L  AL  I+ H L LVG+HMHIGSGVDY HLE
Sbjct: 134 INPGFGHGHSRKTNTGGENSKHGIWHEELDEALACIKAHGLHLVGVHMHIGSGVDYQHLE 193

Query: 203 QVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAAREQIARHLGHP 262
           QV  +M+  +   G D++A S GGGLS PY+  ++ VD + Y   W  AR++I   LGHP
Sbjct: 194 QVARSMIELIGRLGVDIEAFSIGGGLSTPYRSTDKPVDLQRYAQTWAVARKEIEAMLGHP 253

Query: 263 VKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDAGFNDLMRPAMYGSYHHISALAA 322
           V++EIEPGRFLVA+SG L+ +VR+VKQ+G   FV++DAGFNDLMRPAMYG+YH ++ L A
Sbjct: 254 VRMEIEPGRFLVAESGYLVAEVRAVKQVGRNTFVIIDAGFNDLMRPAMYGAYHGMTLLDA 313

Query: 323 DGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRALPEVKAGDYLVLHDTGAYGASM 382
           DG++++  P   TVVAGPLCESGDVFTQ +   +  + LP+ + GD LV+HD GAYGASM
Sbjct: 314 DGQAVDR-PRQPTVVAGPLCESGDVFTQDDQA-LTPQDLPQAQVGDLLVIHDAGAYGASM 371

Query: 383 SSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALE 418
           SSNYNSRPLLPE L +NG  R+IRRRQT+++LL+LE
Sbjct: 372 SSNYNSRPLLPEFLIENGALRMIRRRQTVQDLLSLE 407


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: 579
Number of extensions: 24
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: 410
Length adjustment: 31
Effective length of query: 389
Effective length of database: 379
Effective search space:   147431
Effective search space used:   147431
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 PP_2077 PP_2077 (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.24905.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.3e-123  398.6   0.0   1.5e-123  398.3   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_2077  PP_2077 diaminopimelate decarbox


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2077  PP_2077 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.3   0.0  1.5e-123  1.5e-123      16     416 ..       8     407 ..       3     408 .. 0.95

  Alignments for each domain:
  == domain 1  score: 398.3 bits;  conditional E-value: 1.5e-123
                           TIGR01048  16 lkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgGEleralaA 90 
                                         l+e ++++g+Pl+ yd++t+  r+e+l+ ++     +v +A+KAn nl+vlrl++++Gl ld+vs GE+era aA
  lcl|FitnessBrowser__Putida:PP_2077   8 LAEAVRQHGSPLWAYDTRTIADRVEQLNVFD-----TVRFAQKANPNLHVLRLMRAHGLVLDAVSLGEMERAFAA 77 
                                         567899*********************8776.....59************************************* PP

                           TIGR01048  91 gvk....aekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdaktheyis 161
                                         g++    +  +v++ ++ ++ +le++++++i+ +n++s+++l++l e ++++    rv++R+np++++ ++ +++
  lcl|FitnessBrowser__Putida:PP_2077  78 GASvdgdPAGVVLTCDALDRPTLERVVASKIE-VNAGSIDMLHQLGERSPGH----RVWIRINPGFGHGHSRKTN 147
                                         *9888889***********************9.******************9....******************* PP

                           TIGR01048 162 TGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGG 236
                                         TG ++sK+Gi++e +++ + + +k + l+lvG+h+HIGS++++ +   ++a+ +++l+ +l   g+++e++++GG
  lcl|FitnessBrowser__Putida:PP_2077 148 TGGENSKHGIWHE-ELDEALACIKAHGLHLVGVHMHIGSGVDYQHLE-QVARSMIELIGRL---GVDIEAFSIGG 217
                                         *************.6666777888999*************9876655.5566677888885...*********** PP

                           TIGR01048 237 Glgisyeeeeeapdleeyaeklleklekea.elglklklilEpGRslvanagvlltrVesvKevesrkfvlvDag 310
                                         Gl+ +y++ ++++dl+ ya++++ + ++    lg+ +++ +EpGR+lva++g+l+++V++vK+v+  +fv++Dag
  lcl|FitnessBrowser__Putida:PP_2077 218 GLSTPYRSTDKPVDLQRYAQTWAVARKEIEaMLGHPVRMEIEPGRFLVAESGYLVAEVRAVKQVGRNTFVIIDAG 292
                                         ***************************999899****************************************** PP

                           TIGR01048 311 mndliRpalYeayheiaalkr...leeeetetvdvvGplCEsgDvlakd......relpeveeGdllavasaGAY 376
                                         +ndl+Rpa+Y+ayh +++l++     +++++ + v+GplCEsgDv+++d      ++lp+++ Gdll++++aGAY
  lcl|FitnessBrowser__Putida:PP_2077 293 FNDLMRPAMYGAYHGMTLLDAdgqAVDRPRQPTVVAGPLCESGDVFTQDdqaltpQDLPQAQVGDLLVIHDAGAY 367
                                         ******************987555678899*******************9***999******************* PP

                           TIGR01048 377 gasmssnYnsrprpaevlveegkarlirrretledllale 416
                                         gasmssnYnsrp + e l+e+g +r+irrr+t++dll+le
  lcl|FitnessBrowser__Putida:PP_2077 368 GASMSSNYNSRPLLPEFLIENGALRMIRRRQTVQDLLSLE 407
                                         *************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (410 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: 00:00:00.02
# Mc/sec: 8.36
//
[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