Alignments for a candidate for lysA in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Sinorhizobium medicae WSM419

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate YP_001328203.1 Smed_2538 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>NCBI__GCF_000017145.1:YP_001328203.1
          Length = 422

 Score =  410 bits (1054), Expect = e-119
 Identities = 214/419 (51%), Positives = 291/419 (69%), Gaps = 7/419 (1%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60
           M++F Y+ DG L+AE VPL ++A   GTP Y YS ATLERH+  F ++  D   ++CYA+
Sbjct: 1   MNHFQYR-DGILYAEDVPLTEIARAVGTPFYCYSTATLERHYKVFSQAFADVDAMVCYAM 59

Query: 61  KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120
           KANSN  VL TL RLG+G D+VS GEL R LAAG  PS+++FSGVGKT  EM  AL+  I
Sbjct: 60  KANSNQAVLKTLGRLGAGLDVVSEGELRRALAAGIPPSRIMFSGVGKTAREMDFALEAGI 119

Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180
            CFNVESEPEL+ LN+     G +AP+S RINPDVDA+TH  ISTG ++NKFGI+++RA 
Sbjct: 120 YCFNVESEPELEVLNQRGVRAGKRAPVSFRINPDVDARTHAKISTGKKENKFGISWERAR 179

Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240
            VY  A +LP ++V GID HIGSQ+T L PF DA   L  L+D+L+++G  I H+D+GGG
Sbjct: 180 SVYAHAATLPGIEVTGIDMHIGSQITELQPFDDAFKLLRELVDTLRSDGHVIEHVDLGGG 239

Query: 241 LGVVYRDE--LPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTE 298
           LG+ YR++   PP P  YA  + ++L +  D +++ EPGR I  NAG+LVT+V ++K   
Sbjct: 240 LGIPYREDNNPPPLPDAYADVVKNQL-KGLDCKIVTEPGRLIVGNAGILVTEVVYVKDGG 298

Query: 299 HKNFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTY--DLVGPVCETSDFLGKDRDL 356
            K F I+D AMNDLIRP LY+A+ +I P+R     A     D+VGPVCET D+L  DR++
Sbjct: 299 DKTFVIVDGAMNDLIRPTLYEAYHEIRPVRISAASAPRIKADVVGPVCETGDYLALDREM 358

Query: 357 VL-QEGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESV 414
            + + GDLLA+ S+GAYG   +  YN+R  V EV+V G++ +++R R++   L  L+SV
Sbjct: 359 AMPRAGDLLAIGSAGAYGAVQAGTYNSRLLVPEVLVKGDRFHVIRPRKDYDELIGLDSV 417


Lambda     K      H
   0.319    0.137    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: 466
Number of extensions: 24
Number of successful extensions: 4
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: 417
Length of database: 422
Length adjustment: 32
Effective length of query: 385
Effective length of database: 390
Effective search space:   150150
Effective search space used:   150150
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate YP_001328203.1 Smed_2538 (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.8076.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-148  480.9   0.0   1.4e-148  480.7   0.0    1.0  1  lcl|NCBI__GCF_000017145.1:YP_001328203.1  Smed_2538 diaminopimelate decarb


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017145.1:YP_001328203.1  Smed_2538 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.7   0.0  1.4e-148  1.4e-148       4     415 ..       6     414 ..       3     416 .. 0.97

  Alignments for each domain:
  == domain 1  score: 480.7 bits;  conditional E-value: 1.4e-148
                                 TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaee 72 
                                                +dg l++e+v+l+e+a+  gtP+Y y+++tl+++++ +++af++ +++v+YA+KAnsn avl++l ++
  lcl|NCBI__GCF_000017145.1:YP_001328203.1   6 YRDGILYAEDVPLTEIARAVGTPFYCYSTATLERHYKVFSQAFADVDAMVCYAMKANSNQAVLKTLGRL 74 
                                               57899****************************************999********************* PP

                                 TIGR01048  73 GlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkk 141
                                               G+gldvvs+GEl ralaAg+++++i+fsg+gk+ +e+  ale++i ++nv+s+ ele l++   ++gk+
  lcl|NCBI__GCF_000017145.1:YP_001328203.1  75 GAGLDVVSEGELRRALAAGIPPSRIMFSGVGKTAREMDFALEAGIYCFNVESEPELEVLNQRGVRAGKR 143
                                               ********************************************************************* PP

                                 TIGR01048 142 arvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfve 210
                                               a+v++R+npdvda+th +isTG+ke+KFGi+ e+a+++y  a++l+ +e++Gi++HIGSqi++l+pf +
  lcl|NCBI__GCF_000017145.1:YP_001328203.1 144 APVSFRINPDVDARTHAKISTGKKENKFGISWERARSVYAHAATLPGIEVTGIDMHIGSQITELQPFDD 212
                                               ********************************************************************* PP

                                 TIGR01048 211 aaekvvklleelkeegieleeldlGGGlgisyeeeeeapdl.eeyaeklleklekeaelglklklilEp 278
                                               a++ + +l+++l+++g  +e++dlGGGlgi+y+e++++p l + ya++++++l++     l+ k++ Ep
  lcl|NCBI__GCF_000017145.1:YP_001328203.1 213 AFKLLRELVDTLRSDGHVIEHVDLGGGLGIPYREDNNPPPLpDAYADVVKNQLKG-----LDCKIVTEP 276
                                               **********************************999887615678888888877.....8******** PP

                                 TIGR01048 279 GRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkr.leeeetetvdvvGpl 346
                                               GR +v+nag+l+t+V +vK+ + ++fv+vD++mndliRp lYeayhei++++     +++ ++dvvGp+
  lcl|NCBI__GCF_000017145.1:YP_001328203.1 277 GRLIVGNAGILVTEVVYVKDGGDKTFVIVDGAMNDLIRPTLYEAYHEIRPVRIsAASAPRIKADVVGPV 345
                                               **************************************************964356678899******* PP

                                 TIGR01048 347 CEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllal 415
                                               CE+gD la dre+   ++Gdlla+ saGAYga  + +Ynsr  + evlv++++ ++ir r+ +++l+ l
  lcl|NCBI__GCF_000017145.1:YP_001328203.1 346 CETGDYLALDREMAMPRAGDLLAIGSAGAYGAVQAGTYNSRLLVPEVLVKGDRFHVIRPRKDYDELIGL 414
                                               *****************************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (422 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: 12.40
//
[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