Alignments for a candidate for lysA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Stenotrophomonas chelatiphaga DSM 21508

Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate WP_057507033.1 ABB28_RS02115 diaminopimelate decarboxylase

Query= reanno::Dyella79:N515DRAFT_4002
         (853 letters)



>NCBI__GCF_001431535.1:WP_057507033.1
          Length = 864

 Score =  863 bits (2229), Expect = 0.0
 Identities = 474/860 (55%), Positives = 589/860 (68%), Gaps = 15/860 (1%)

Query: 1   MKFGGTSVATLPRWQNIRELVASRRAE-GARVLVVVSALTGITDALKQMC-AQEDKGKRV 58
           +KFGGTSV+   RW  I +L   R  E G+RVLVVVSAL+G+T+ L  +     D   RV
Sbjct: 13  LKFGGTSVSRRHRWDTIGKLAKKRAEETGSRVLVVVSALSGVTNELTAIADGAADSRARV 72

Query: 59  EAARAIAQRHYDLLDHMQLAVPATLAERLSELAMLAEDGPGAMGELAWAALVQAHGELMS 118
            A   + +RH   LD ++L   A L ERL+ L  L +D   A   L W A V   GEL+S
Sbjct: 73  AA---LVERHQAFLDELELP-RAVLGERLAALQALLDDARAAARTLDWQAEVLGQGELLS 128

Query: 119 SALGAAFLSHAGLPTEWLDARDCLAAVA-LPNQNERTKLLSAMVEARPDPALNARL-AEL 176
           S++GAA+L   GL   W+DAR  L A+  LPNQ+  ++ LS   + + D A   R  A+ 
Sbjct: 129 SSIGAAYLHQNGLDMGWMDARQWLDALPPLPNQSPWSQRLSVNCQWKSDEAWAQRFRAQP 188

Query: 177 GEVFITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVP 236
             + ITQGFIAR A G T +LGRGGSDTSA+YFGALL A RVEIWTDV GMF+ANP+ VP
Sbjct: 189 TRLLITQGFIARHADGGTAILGRGGSDTSAAYFGALLGASRVEIWTDVPGMFSANPKDVP 248

Query: 237 GARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVRE 296
            ARLL RLDY EAQEIA+TGAKVLHPR + P R+  VPM I DT RPEL GT I      
Sbjct: 249 DARLLTRLDYYEAQEIATTGAKVLHPRSIKPCRDAGVPMAILDTERPELPGTSIDGSAAP 308

Query: 297 HAPSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSLD 356
             P VKAIS R GI LVSME +GMWQQVGFLADVF  FK+HGLSVDLIGSAETNVTVSLD
Sbjct: 309 -VPGVKAISRRNGIVLVSMEGIGMWQQVGFLADVFGLFKKHGLSVDLIGSAETNVTVSLD 367

Query: 357 PTENLLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQIRVH 416
           P+ENL+++D +AAL++DL+++C+VK+I PCAAITLVGRGMRS+LH LS V A FG+ RVH
Sbjct: 368 PSENLVNTDVLAALSADLSQICKVKIIVPCAAITLVGRGMRSLLHKLSDVWATFGRERVH 427

Query: 417 LISQSSNNLNLTFVVDENVVDDLLPHLHELLIAAGALRTDDSALFGPSWQALYGSGEVAA 476
           +ISQSSN+LNLTFV+DE   D LLP LH  LI +GA+  +++A+FGP W+ +  +G V  
Sbjct: 428 MISQSSNDLNLTFVIDETDADGLLPILHAELIDSGAMPVEETAVFGPRWREI--AGTVRP 485

Query: 477 PAASWWRTAERERLLRLGAERTPRYVYHLPTVRQQARELKSLGAVDRLHYAVKANTHPAI 536
               WWR  +R  LL+L    TPRYVYHLPTVR +AR L ++  +D+ +YA+KAN+HPAI
Sbjct: 486 RGTPWWR-GQRAHLLQLAEAGTPRYVYHLPTVRARARALAAITPIDQRYYAIKANSHPAI 544

Query: 537 LKALAEEGFGFECVSPGELKAVLAAVPESAP--LLFTPNFAPRADYEWALTTRATISLDA 594
           L+ L  EGFG ECVS GELK V   +P  +P  +LFTP+F PR ++E A     T+++D 
Sbjct: 545 LETLEAEGFGLECVSHGELKHVFNVLPGLSPRRVLFTPSFCPREEFEAAFALGVTVTVDN 604

Query: 595 LYQLENWGELFRGREIVLRVDLGRGLGHHEKVRTGGSGSKFGLPVELVDSFLRLADAHGV 654
           +  L+ W +LFR RE+ LRVDLGRG GHH KVRTGG  SKFGLP+  VD F+R A   G 
Sbjct: 605 VEALQRWPDLFRNRELWLRVDLGRGEGHHAKVRTGGKESKFGLPMARVDEFVRAATELGT 664

Query: 655 IVRGLHAHLGSGILDEGHWGEVYGQLASLAERIGSVAFLDIGGGLGVPSHPGEARLDIAA 714
            + GLHAHLGSG+    HW  +  +LA  A RIG+V  +DIGGG+ +P    +   D+ A
Sbjct: 665 TIVGLHAHLGSGVETAQHWRLMCDELAGFARRIGTVQTIDIGGGMPIPYSEEDEPFDLEA 724

Query: 715 LDRVLRSVKAAYPHYQLWMEPGRYLVADAGVLLARVTQQKGKGSWRYLGVDTGMNSLIRP 774
               L  VKA +P ++L +EPGRYLVA++GVLL R TQ   K   R +G+D GMN+LIRP
Sbjct: 725 WAEGLAEVKAVHPAFRLAIEPGRYLVAESGVLLTRCTQVVEKEGVRRVGLDAGMNTLIRP 784

Query: 775 ALYEAWHEIVNLTRLDEPATGLFQVVGPICESGDVLGTDRRLP-EAQEGDVVLVAQAGAY 833
           ALY+AWH+I NL+R    A   F VVGPICES DV G  R+LP      DV++VA AGAY
Sbjct: 785 ALYDAWHDIENLSRQGGYAEAAFDVVGPICESSDVFGKRRKLPASTAPDDVMVVADAGAY 844

Query: 834 GKVMSSPYNMRDEAEEVILD 853
           G VM+S YN R    E IL+
Sbjct: 845 GYVMASTYNQRAMPREDILE 864


Lambda     K      H
   0.319    0.135    0.398 

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: 1866
Number of extensions: 87
Number of successful extensions: 9
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: 853
Length of database: 864
Length adjustment: 42
Effective length of query: 811
Effective length of database: 822
Effective search space:   666642
Effective search space used:   666642
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: 56 (26.2 bits)

Align candidate WP_057507033.1 ABB28_RS02115 (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.12077.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    7.4e-96  307.1   0.0    9.9e-96  306.7   0.0    1.1  1  lcl|NCBI__GCF_001431535.1:WP_057507033.1  ABB28_RS02115 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057507033.1  ABB28_RS02115 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.7   0.0   9.9e-96   9.9e-96      16     392 ..     498     860 ..     492     864 .] 0.93

  Alignments for each domain:
  == domain 1  score: 306.7 bits;  conditional E-value: 9.9e-96
                                 TIGR01048  16 lkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgGEl 84 
                                               l +la e gtP Yvy   t+r+r++al++       +  YA+KAns  a+l++l++eG+gl++vs+GEl
  lcl|NCBI__GCF_001431535.1:WP_057507033.1 498 LLQLA-EAGTPRYVYHLPTVRARARALAAITPI--DQRYYAIKANSHPAILETLEAEGFGLECVSHGEL 563
                                               55665.46*******************999875..478******************************* PP

                                 TIGR01048  85 era..laAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpd 151
                                               + +  +  g ++ +++f+     +ee+eaa +l+++ + vd+ve l+++ ++ ++     +++lRv  +
  lcl|NCBI__GCF_001431535.1:WP_057507033.1 564 KHVfnVLPGLSPRRVLFTPSFCPREEFEAAFALGVT-VTVDNVEALQRWPDLFRNR----ELWLRVDLG 627
                                               *9833567999************************8.************8888887....********* PP

                                 TIGR01048 152 vdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklle 220
                                                +  +h ++ TG kesKFG+ +++  e +++a++l   ++vG+h+H+GS+++ ++  + ++++++ +++
  lcl|NCBI__GCF_001431535.1:WP_057507033.1 628 RGEGHHAKVRTGGKESKFGLPMARVDEFVRAATELG-TTIVGLHAHLGSGVETAQHWRLMCDELAGFAR 695
                                               ***********************8888887777776.89****************************** PP

                                 TIGR01048 221 elkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvl 289
                                               +      +++++d+GGG+ i+y+ee+e+ dle +ae l+ +++    +    +l +EpGR+lva++gvl
  lcl|NCBI__GCF_001431535.1:WP_057507033.1 696 R----IGTVQTIDIGGGMPIPYSEEDEPFDLEAWAEGLA-EVKA---VHPAFRLAIEPGRYLVAESGVL 756
                                               *....699*****************************77.5555...45699***************** PP

                                 TIGR01048 290 ltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdre 358
                                               ltr ++v e+e  + v  Dagmn+liRpalY+a+h+i +l+r+   +++ +dvvGp+CEs+Dv++k r+
  lcl|NCBI__GCF_001431535.1:WP_057507033.1 757 LTRCTQVVEKEGVRRVGLDAGMNTLIRPALYDAWHDIENLSRQGGYAEAAFDVVGPICESSDVFGKRRK 825
                                               ******999999999****************************************************** PP

                                 TIGR01048 359 lp.eveeGdllavasaGAYgasmssnYnsrprpae 392
                                               lp ++ ++d+++va+aGAYg+ m+s+Yn+r+ p+e
  lcl|NCBI__GCF_001431535.1:WP_057507033.1 826 LPaSTAPDDVMVVADAGAYGYVMASTYNQRAMPRE 860
                                               **77899***********************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (864 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 15.46
//
[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