Alignments for a candidate for lysA in Halorhodospira halophila SL1

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Halorhodospira halophila SL1

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_011813997.1 HHAL_RS06105 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>NCBI__GCF_000015585.1:WP_011813997.1
          Length = 418

 Score =  419 bits (1077), Expect = e-122
 Identities = 213/407 (52%), Positives = 284/407 (69%), Gaps = 2/407 (0%)

Query: 11  QLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAVKANSNLGVLN 70
           +LWAE +PL +LA ++GTP YVYSRA +E  W  +  ++G     +CYAVKAN NL +L 
Sbjct: 13  RLWAEALPLDELAERFGTPCYVYSRAAIEERWALYRSALGVAGD-VCYAVKANGNLALLQ 71

Query: 71  TLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKIKCFNVESEPE 130
            LAR G+GFDIVS GELERVL AGGD ++VVFSGVGK   E++RALQ  I+CFNVES  E
Sbjct: 72  LLARHGAGFDIVSGGELERVLHAGGDAARVVFSGVGKGTDEIRRALQAGIRCFNVESAAE 131

Query: 131 LQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAAQVYRLAHSLP 190
           L+R+  VA      AP++LR+NPDV+ +THPYI+TGL  +KFGI  + A  +Y  A + P
Sbjct: 132 LERIASVAATENTPAPVALRVNPDVNPETHPYIATGLAQSKFGIALEEAEALYLQAANDP 191

Query: 191 NLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGGLGVVYRDELP 250
            L+V GI CHIGSQL ++AP  +A +RL AL   L+ +GI + H+D GGGLGV Y DE P
Sbjct: 192 RLEVRGIACHIGSQLLSVAPLTEAAERLAALARRLQEQGISLDHIDAGGGLGVHYIDEQP 251

Query: 251 PQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHKNFAIIDAAMN 310
           P P+E+ +A+   L R   + ++ EPGRAI A AG+L+T++E+LKH   K FAI+DA MN
Sbjct: 252 PTPAEHIEAISAPL-RDLGVSVLVEPGRAIVAEAGILLTRIEYLKHNGGKEFAIVDAGMN 310

Query: 311 DLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQEGDLLAVRSSG 370
           D +RPALY A   +  + P + E +  D+VGPVCE++D   +D  L    G LLA+RS+G
Sbjct: 311 DYLRPALYDAAHTLEAVTPSEAELRPVDVVGPVCESADTFARDCTLPAAAGGLLAIRSAG 370

Query: 371 AYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLPE 417
           AYG  M+S YN RPR  EV+VDG + +L+R+RE +  L + ES+LPE
Sbjct: 371 AYGAVMASQYNARPRPPEVLVDGTQAHLIRRRETIDELMSGESLLPE 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: 485
Number of extensions: 20
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: 417
Length of database: 418
Length adjustment: 32
Effective length of query: 385
Effective length of database: 386
Effective search space:   148610
Effective search space used:   148610
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 WP_011813997.1 HHAL_RS06105 (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.12400.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.3e-153  495.1   0.0   7.4e-153  494.9   0.0    1.0  1  lcl|NCBI__GCF_000015585.1:WP_011813997.1  HHAL_RS06105 diaminopimelate dec


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015585.1:WP_011813997.1  HHAL_RS06105 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.9   0.0  7.4e-153  7.4e-153       8     416 ..      13     412 ..       8     413 .. 0.98

  Alignments for each domain:
  == domain 1  score: 494.9 bits;  conditional E-value: 7.4e-153
                                 TIGR01048   8 eleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgl 76 
                                               +l++e+ +l elae+fgtP Yvy++++++er++ +++a + +   v+YAvKAn nla+l+lla++G+g+
  lcl|NCBI__GCF_000015585.1:WP_011813997.1  13 RLWAEALPLDELAERFGTPCYVYSRAAIEERWALYRSALGVA-GDVCYAVKANGNLALLQLLARHGAGF 80 
                                               689999*********************************864.68************************ PP

                                 TIGR01048  77 dvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvl 145
                                               d+vsgGEler+l+Ag +a ++vfsg+gk ++e+++al+++i+++nv+s +ele++ ++a+  ++ a+v+
  lcl|NCBI__GCF_000015585.1:WP_011813997.1  81 DIVSGGELERVLHAGGDAARVVFSGVGKGTDEIRRALQAGIRCFNVESAAELERIASVAATENTPAPVA 149
                                               ********************************************************************* PP

                                 TIGR01048 146 lRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaek 214
                                               lRvnpdv+++th+yi+TGl++sKFGi++eeae+ y +a++++ le+ Gi +HIGSq+l ++p++eaae+
  lcl|NCBI__GCF_000015585.1:WP_011813997.1 150 LRVNPDVNPETHPYIATGLAQSKFGIALEEAEALYLQAANDPRLEVRGIACHIGSQLLSVAPLTEAAER 218
                                               ********************************************************************* PP

                                 TIGR01048 215 vvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslv 283
                                               ++ l+++l+e+gi+l ++d+GGGlg++y +e+ +p+++e  e++ + l++     l +++++EpGR++v
  lcl|NCBI__GCF_000015585.1:WP_011813997.1 219 LAALARRLQEQGISLDHIDAGGGLGVHYIDEQ-PPTPAEHIEAISAPLRD-----LGVSVLVEPGRAIV 281
                                               ******************************99.***************99.....799*********** PP

                                 TIGR01048 284 anagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDv 352
                                               a+ag+lltr+e++K+++ ++f++vDagmnd +RpalY+a h + a+ + +e+e   vdvvGp+CEs+D+
  lcl|NCBI__GCF_000015585.1:WP_011813997.1 282 AEAGILLTRIEYLKHNGGKEFAIVDAGMNDYLRPALYDAAHTLEAV-TPSEAELRPVDVVGPVCESADT 349
                                               **********************************************.668888**************** PP

                                 TIGR01048 353 lakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                               +a+d +lp++  G lla++saGAYga m+s+Yn+rprp evlv++ +a+lirrret+++l++ e
  lcl|NCBI__GCF_000015585.1:WP_011813997.1 350 FARDCTLPAAA-GGLLAIRSAGAYGAVMASQYNARPRPPEVLVDGTQAHLIRRRETIDELMSGE 412
                                               ********998.************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (418 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: 00:00:00.02
# Mc/sec: 7.71
//
[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