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

GapMind for Amino acid biosynthesis

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

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate Ac3H11_3862 Diaminopimelate decarboxylase (EC 4.1.1.20)

Query= BRENDA::P00861
         (420 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3862
          Length = 414

 Score =  551 bits (1421), Expect = e-161
 Identities = 274/406 (67%), Positives = 323/406 (79%), Gaps = 6/406 (1%)

Query: 17  LLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIHILRLMREQGVKVDSVS 76
           L  L  +FG P+WVYDA  IR++IA +  F+ +RFAQKACSNIHIL+LMREQGVKVD+VS
Sbjct: 10  LWALADQFGTPLWVYDAATIRQRIAQVSNFETIRFAQKACSNIHILKLMREQGVKVDAVS 69

Query: 77  LGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVSPG 136
            GEI RALAAGY     P +IVFTAD+ D ATL+ V E  +PVNAGS+DML QLG  SPG
Sbjct: 70  RGEILRALAAGYVAGGEPSEIVFTADLFDAATLDCVVEHGVPVNAGSIDMLHQLGARSPG 129

Query: 137 HRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGSGV 196
           H VWLR+NPGFGHGHS KTNTGGE+SKHGIW+TDLPAAL  I++H L+LVG+HMHIGSGV
Sbjct: 130 HAVWLRINPGFGHGHSNKTNTGGEHSKHGIWHTDLPAALAAIKQHGLKLVGLHMHIGSGV 189

Query: 197 DYAHLEQVCGAM---VRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAARE 253
           DY+HL++VCGAM   VR     G DL AISAGGGLS+PY+ G+  VDT+HY+GLW+AAR+
Sbjct: 190 DYSHLQEVCGAMVNLVRTAHAAGHDLHAISAGGGLSIPYRSGDPVVDTQHYHGLWDAARQ 249

Query: 254 QIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDAGFNDLMRPAMYGS 313
           Q    +GH + LEIEPGRFLVA+SGVL+ QVR+ K  G+ HFVLVD GFN+LMRP+MYGS
Sbjct: 250 QAEAIVGHKLGLEIEPGRFLVAESGVLLGQVRATKDAGNNHFVLVDTGFNELMRPSMYGS 309

Query: 314 YHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRALPEVKAGDYLVLH 373
           YH +S L  DG      P   +VVAGPLCESGDVFTQ +GG V  R LP  + GD LV+H
Sbjct: 310 YHAMSVLRRDGTQAAEQP---SVVAGPLCESGDVFTQGDGGVVLPRDLPAAQVGDLLVIH 366

Query: 374 DTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALEL 419
           DTGAYGASMSSNYN+RPL+ EVL D GQARLIRRRQT++ELLALE+
Sbjct: 367 DTGAYGASMSSNYNTRPLIAEVLVDGGQARLIRRRQTVDELLALEI 412


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: 668
Number of extensions: 25
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: 414
Length adjustment: 31
Effective length of query: 389
Effective length of database: 383
Effective search space:   148987
Effective search space used:   148987
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 Ac3H11_3862 (Diaminopimelate decarboxylase (EC 4.1.1.20))
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.20749.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.4e-132  428.1   0.0   1.7e-132  427.8   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3862  Diaminopimelate decarboxylase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3862  Diaminopimelate decarboxylase (EC 4.1.1.20)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.8   0.0  1.7e-132  1.7e-132      15     416 ..       9     411 ..       5     412 .. 0.95

  Alignments for each domain:
  == domain 1  score: 427.8 bits;  conditional E-value: 1.7e-132
                                        TIGR01048  15 dlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgl 76 
                                                      +l +la++fgtPl+vyd++t+r+r+++++++      ++ +A+KA+sn+++l+l++e+G+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3862   9 QLWALADQFGTPLWVYDAATIRQRIAQVSNFE-----TIRFAQKACSNIHILKLMREQGVKV 65 
                                                      6778***********************99876.....69*********************** PP

                                        TIGR01048  77 dvvsgGEleralaAgvk....aekivfsgngkseeeleaaleleiklinvdsveelelleei 134
                                                      d+vs GE+ ralaAg+     +++ivf+++  + ++l  ++e+++  +n++s+++l++l + 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3862  66 DAVSRGEILRALAAGYVaggePSEIVFTADLFDAATLDCVVEHGVP-VNAGSIDMLHQLGAR 126
                                                      *************99877777************************9.*************99 PP

                                        TIGR01048 135 akelgkkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihv 196
                                                      ++++     v+lR+np++++ ++++++TG ++sK+Gi+++ +++a+ +a+k++ l+lvG+h+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3862 127 SPGH----AVWLRINPGFGHGHSNKTNTGGEHSKHGIWHT-DLPAALAAIKQHGLKLVGLHM 183
                                                      9999....9******************************9.9999***************** PP

                                        TIGR01048 197 HIGSqildlepfveaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaekl 258
                                                      HIGS++++ +  + + ++ v+l+++ +++g +l+++++GGGl+i+y++ +  +d+++y   +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3862 184 HIGSGVDYSHLQEVCGAM-VNLVRTAHAAGHDLHAISAGGGLSIPYRSGDPVVDTQHYHGLW 244
                                                      ******887776666665.57777879*********************************** PP

                                        TIGR01048 259 leklekea.elglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpal 319
                                                       ++ +++   +g+kl l +EpGR+lva++gvll +V+++K++++ +fvlvD+g+n+l+Rp++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3862 245 DAARQQAEaIVGHKLGLEIEPGRFLVAESGVLLGQVRATKDAGNNHFVLVDTGFNELMRPSM 306
                                                      ****999878999************************************************* PP

                                        TIGR01048 320 Yeayheiaalkr.leeeetetvdvvGplCEsgDvlakd.......relpeveeGdllavasa 373
                                                      Y++yh +++l+r  ++++++   v+GplCEsgDv+++        r+lp+++ Gdll+++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3862 307 YGSYHAMSVLRRdGTQAAEQPSVVAGPLCESGDVFTQGdggvvlpRDLPAAQVGDLLVIHDT 368
                                                      **********98445667888999*************99*********************** PP

                                        TIGR01048 374 GAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                                      GAYgasmssnYn+rp +aevlv++g+arlirrr+t+++llale
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3862 369 GAYGASMSSNYNTRPLIAEVLVDGGQARLIRRRQTVDELLALE 411
                                                      ****************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (414 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: 9.07
//
[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