Alignments for a candidate for lysA in Klebsiella variicola At-22

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Klebsiella variicola At-22

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_008806341.1 KVAR_RS04100 diaminopimelate decarboxylase

Query= BRENDA::P00861
         (420 letters)



>NCBI__GCF_000025465.1:WP_008806341.1
          Length = 420

 Score =  758 bits (1956), Expect = 0.0
 Identities = 367/420 (87%), Positives = 397/420 (94%)

Query: 1   MPHSLFSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIH 60
           MPHSL++TDTDLTA+NLLRLPAEFGCPVWVYDAQIIRRQIA L QFDVVRFAQKACSNIH
Sbjct: 1   MPHSLYATDTDLTADNLLRLPAEFGCPVWVYDAQIIRRQIAQLSQFDVVRFAQKACSNIH 60

Query: 61  ILRLMREQGVKVDSVSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVN 120
           ILRLMREQGVKVDSVSLGEIERALAAGY+PQ +P+DIVFTAD+ID ATL+RV  LQIPVN
Sbjct: 61  ILRLMREQGVKVDSVSLGEIERALAAGYDPQQNPEDIVFTADLIDDATLDRVKALQIPVN 120

Query: 121 AGSVDMLDQLGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQR 180
           AGS+DML QLG+VSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWY+ LPAAL+V++R
Sbjct: 121 AGSIDMLSQLGEVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYSHLPAALEVMRR 180

Query: 181 HHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVD 240
           + LQLVGIHMHIGSGVDY HLEQVCGAMVRQV++FGQDLQAISAGGGLS+PY++GEEA+D
Sbjct: 181 YQLQLVGIHMHIGSGVDYGHLEQVCGAMVRQVVDFGQDLQAISAGGGLSIPYREGEEAID 240

Query: 241 TEHYYGLWNAAREQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDA 300
           T HYYGLWN AREQIA HLGHPVKLEIEPGRFLVA+SGVL++QVRSVK+MGSRHFVL+DA
Sbjct: 241 TAHYYGLWNRAREQIAAHLGHPVKLEIEPGRFLVAESGVLVSQVRSVKEMGSRHFVLIDA 300

Query: 301 GFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRA 360
           GFNDLMRPAMYGSYHHI+ALAADGR L  AP VETVVAGPLCESGDVFTQQEGG VETR 
Sbjct: 301 GFNDLMRPAMYGSYHHITALAADGRDLSAAPQVETVVAGPLCESGDVFTQQEGGKVETRL 360

Query: 361 LPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELL 420
           LP V  GDYLVLHDTGAYGASMSSNYNSRPLLPEVLFD G+ARLIRRRQTI+ELLALEL+
Sbjct: 361 LPAVVPGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDGGKARLIRRRQTIQELLALELI 420


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: 736
Number of extensions: 24
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: 420
Length adjustment: 32
Effective length of query: 388
Effective length of database: 388
Effective search space:   150544
Effective search space used:   150544
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_008806341.1 KVAR_RS04100 (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.19131.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-141  458.1   0.0   1.3e-141  457.8   0.0    1.0  1  lcl|NCBI__GCF_000025465.1:WP_008806341.1  KVAR_RS04100 diaminopimelate dec


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025465.1:WP_008806341.1  KVAR_RS04100 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.8   0.0  1.3e-141  1.3e-141       7     416 ..       8     418 ..       3     419 .. 0.97

  Alignments for each domain:
  == domain 1  score: 457.8 bits;  conditional E-value: 1.3e-141
                                 TIGR01048   7 geleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlg 75 
                                               +++++++ +l +l +efg+P++vyd++ +r+++++l++++     +v +A+KA+sn+++lrl++e+G++
  lcl|NCBI__GCF_000025465.1:WP_008806341.1   8 TDTDLTADNLLRLPAEFGCPVWVYDAQIIRRQIAQLSQFD-----VVRFAQKACSNIHILRLMREQGVK 71 
                                               67788999*****************************998.....79********************** PP

                                 TIGR01048  76 ldvvsgGEleralaAgvk....aekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgk 140
                                               +d+vs GE+eralaAg++    +e+ivf+++ +++++l ++ +l+i  +n++s+++l++l e+++++  
  lcl|NCBI__GCF_000025465.1:WP_008806341.1  72 VDSVSLGEIERALAAGYDpqqnPEDIVFTADLIDDATLDRVKALQIP-VNAGSIDMLSQLGEVSPGH-- 137
                                               *****************9889999**********************9.*******************.. PP

                                 TIGR01048 141 karvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfv 209
                                                 rv+lRvnp++++ ++++++TG ++sK+Gi+++ +++a+  ++++ +l+lvGih+HIGS++++ +  +
  lcl|NCBI__GCF_000025465.1:WP_008806341.1 138 --RVWLRVNPGFGHGHSQKTNTGGENSKHGIWYS-HLPAALEVMRRYQLQLVGIHMHIGSGVDYGHLEQ 203
                                               ..********************************.8899999999999********************* PP

                                 TIGR01048 210 eaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekea.elglklklilE 277
                                                + ++v ++++     g++l+++++GGGl+i+y+e eea+d+++y+  ++++ e+ a +lg+ +kl +E
  lcl|NCBI__GCF_000025465.1:WP_008806341.1 204 VCGAMVRQVVDF----GQDLQAISAGGGLSIPYREGEEAIDTAHYYGLWNRAREQIAaHLGHPVKLEIE 268
                                               ************....9***************************************99*********** PP

                                 TIGR01048 278 pGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkr....leeeetetvdv 342
                                               pGR+lva++gvl+ +V+svKe++sr+fvl+Dag+ndl+Rpa+Y++yh+i+al++    l++++++++ v
  lcl|NCBI__GCF_000025465.1:WP_008806341.1 269 PGRFLVAESGVLVSQVRSVKEMGSRHFVLIDAGFNDLMRPAMYGSYHHITALAAdgrdLSAAPQVETVV 337
                                               ***************************************************9877777999******** PP

                                 TIGR01048 343 vGplCEsgDvlakd.......relpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlir 404
                                               +GplCEsgDv++++       r lp+v +Gd+l+++++GAYgasmssnYnsrp + evl+++gkarlir
  lcl|NCBI__GCF_000025465.1:WP_008806341.1 338 AGPLCESGDVFTQQeggkvetRLLPAVVPGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDGGKARLIR 406
                                               ********************999********************************************** PP

                                 TIGR01048 405 rretledllale 416
                                               rr+t+++llale
  lcl|NCBI__GCF_000025465.1:WP_008806341.1 407 RRQTIQELLALE 418
                                               *********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (420 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.39
//
[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