Alignments for a candidate for lysA in Burkholderia vietnamiensis G4

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Burkholderia vietnamiensis G4

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_011882634.1 diaminopimelate decarboxylase

Query= BRENDA::P00861
         (420 letters)



>NCBI__GCF_000016205.1:WP_011882634.1
          Length = 412

 Score =  537 bits (1383), Expect = e-157
 Identities = 259/407 (63%), Positives = 316/407 (77%)

Query: 12  LTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIHILRLMREQGVK 71
           L +  L  L  ++G P+WVYDA +IR +IA L+QFDV+R+AQKA SN+HIL+LMRE+G  
Sbjct: 3   LDSRQLATLAQQYGTPLWVYDADVIRERIAQLRQFDVIRYAQKANSNLHILKLMREEGAC 62

Query: 72  VDSVSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLG 131
           VD+VSLGEIER+LAAG++P   P+ +VFTAD+ID+ TL  V +  + VNAGS+DML ++G
Sbjct: 63  VDAVSLGEIERSLAAGFSPAGEPEGVVFTADLIDRPTLAAVLKHGVTVNAGSLDMLARVG 122

Query: 132 QVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMH 191
           + +PGHRVWLRVNPGFGHGHS KTNTGG  SKHGIW  D+P A++++ R+ L+LVGIHMH
Sbjct: 123 EHAPGHRVWLRVNPGFGHGHSNKTNTGGPQSKHGIWIDDVPRAIEIVHRYGLKLVGIHMH 182

Query: 192 IGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAA 251
           IGSGVDY HL QVC AMV  V   G D+ AISAGGGLS+PY+ GE  VD  HY+  W+AA
Sbjct: 183 IGSGVDYGHLSQVCDAMVDLVTSLGHDIDAISAGGGLSIPYRDGEPRVDVGHYFNQWDAA 242

Query: 252 REQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDAGFNDLMRPAMY 311
           R++I RHLGH V++EIEPGRFLVA++G L+T+V++V +     FVL+DAGFNDLMRP+MY
Sbjct: 243 RKRIERHLGHAVRIEIEPGRFLVAEAGTLVTEVQAVNRRPQHDFVLIDAGFNDLMRPSMY 302

Query: 312 GSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRALPEVKAGDYLV 371
           GSYH +S  A DG      P V+  +AGPLCESGDVFTQ  GG V  R LP+ + GD L 
Sbjct: 303 GSYHAVSVHAPDGTLPAGRPLVDIAIAGPLCESGDVFTQDAGGVVTHRKLPQPQIGDLLF 362

Query: 372 LHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALE 418
           LHD GAYGASMSSNYNSRPL PEVL D G  RLIRRRQTI ELLALE
Sbjct: 363 LHDAGAYGASMSSNYNSRPLAPEVLVDRGTPRLIRRRQTIGELLALE 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: 645
Number of extensions: 31
Number of successful extensions: 1
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: 412
Length adjustment: 31
Effective length of query: 389
Effective length of database: 381
Effective search space:   148209
Effective search space used:   148209
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 WP_011882634.1 (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.3715.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-127  410.6   0.0   3.1e-127  410.5   0.0    1.0  1  lcl|NCBI__GCF_000016205.1:WP_011882634.1  diaminopimelate decarboxylase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016205.1:WP_011882634.1  diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.5   0.0  3.1e-127  3.1e-127      11     416 ..       3     409 ..       1     410 [. 0.95

  Alignments for each domain:
  == domain 1  score: 410.5 bits;  conditional E-value: 3.1e-127
                                 TIGR01048  11 iegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvv 79 
                                               ++  +l++la+++gtPl+vyd++ +rer+++l++++     ++ YA+KAnsnl++l+l++eeG+++d+v
  lcl|NCBI__GCF_000016205.1:WP_011882634.1   3 LDSRQLATLAQQYGTPLWVYDADVIRERIAQLRQFD-----VIRYAQKANSNLHILKLMREEGACVDAV 66 
                                               6778999***************************98.....79************************** PP

                                 TIGR01048  80 sgGEleralaAgvk....aekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarv 144
                                               s GE+er laAg++    +e +vf+++ +++ +l+a+l+++++ +n++s+++l+++ e a+++    rv
  lcl|NCBI__GCF_000016205.1:WP_011882634.1  67 SLGEIERSLAAGFSpagePEGVVFTADLIDRPTLAAVLKHGVT-VNAGSLDMLARVGEHAPGH----RV 130
                                               *************989999***********************8.*******************....** PP

                                 TIGR01048 145 llRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaae 213
                                               +lRvnp++++ ++++++TG  +sK+Gi++++  +a+e +++   l+lvGih+HIGS++++ +  + +++
  lcl|NCBI__GCF_000016205.1:WP_011882634.1 131 WLRVNPGFGHGHSNKTNTGGPQSKHGIWIDDVPRAIEIVHRYG-LKLVGIHMHIGSGVDYGHLSQ-VCD 197
                                               ******************************9999999887765.**************8877655.566 PP

                                 TIGR01048 214 kvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekea.elglklklilEpGRs 281
                                                +v+l+++l   g ++ ++++GGGl+i+y++ e  +d+ +y +++ ++ ++   +lg+ +++ +EpGR+
  lcl|NCBI__GCF_000016205.1:WP_011882634.1 198 AMVDLVTSL---GHDIDAISAGGGLSIPYRDGEPRVDVGHYFNQWDAARKRIErHLGHAVRIEIEPGRF 263
                                               677888885...***************************************999*************** PP

                                 TIGR01048 282 lvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkr....leeeetetvdvvGpl 346
                                               lva+ag+l+t+V++v +++++ fvl+Dag+ndl+Rp++Y++yh +++ +        ++ + + ++Gpl
  lcl|NCBI__GCF_000016205.1:WP_011882634.1 264 LVAEAGTLVTEVQAVNRRPQHDFVLIDAGFNDLMRPSMYGSYHAVSVHAPdgtlPAGRPLVDIAIAGPL 332
                                               **********************************************9987666667788999******* PP

                                 TIGR01048 347 CEsgDvlakd.......relpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrret 408
                                               CEsgDv+++d       r+lp+ + Gdll +++aGAYgasmssnYnsrp + evlv+ g  rlirrr+t
  lcl|NCBI__GCF_000016205.1:WP_011882634.1 333 CESGDVFTQDaggvvthRKLPQPQIGDLLFLHDAGAYGASMSSNYNSRPLAPEVLVDRGTPRLIRRRQT 401
                                               ********************************************************************* PP

                                 TIGR01048 409 ledllale 416
                                               + +llale
  lcl|NCBI__GCF_000016205.1:WP_011882634.1 402 IGELLALE 409
                                               *****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (412 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: 7.32
//
[ok]

This GapMind analysis is from Apr 10 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