Alignments for a candidate for lysA in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Nitriliruptor alkaliphilus DSM 45188

Align diaminopimelate decarboxylase subunit (EC 4.1.1.20) (characterized)
to candidate WP_052666188.1 NITAL_RS10480 diaminopimelate decarboxylase

Query= metacyc::MONOMER-6601
         (439 letters)



>NCBI__GCF_000969705.1:WP_052666188.1
          Length = 433

 Score =  385 bits (988), Expect = e-111
 Identities = 204/431 (47%), Positives = 279/431 (64%), Gaps = 7/431 (1%)

Query: 6   TSRQNQHGHLEIGGVDALYLAEKYGTPLYVYDVALIRERAKSFKQAFISAGLKAQVAYAS 65
           T+ +++ G L IGG     LA  +GTPL+V D A +RER + +   F        VAYAS
Sbjct: 8   TAERDEDGVLHIGGAAVTDLARDHGTPLWVVDEADLRERCRRYVTGFPGV----DVAYAS 63

Query: 66  KAFSSVAMIQLAEEEGLSLDVVSGGELYTAVAAGF-PAERIHFHGNNKSREELRMALEHR 124
           KA+ +V ++QL E+EGL +DV S GEL+TA+ AG  PA+ IH HGNNK   EL +AL+  
Sbjct: 64  KAWCTVGLLQLVEDEGLLVDVASEGELHTALVAGVDPAKLIH-HGNNKGDAELDLALKVG 122

Query: 125 IGCIVVDNFYEIALLEDLCKETGHSIDVLLRITPGVEAHTHDYITTGQEDSKFGFDLHNG 184
           +G IVVD+F E+  LE L         V LRITPG++AHTH+Y+ TG +D+KFGF L  G
Sbjct: 123 LGRIVVDSFDELDRLERLAAARDIVAQVWLRITPGIDAHTHEYVRTGHDDAKFGFTLSLG 182

Query: 185 QTERAIEQVLQSEHIQLLGVHCHIGSQIFDTAGFVLAAEKIFKKLDEWRDSYSFVSKVLN 244
             + A+      EHI+++G+H HIGSQIF T  F+  A+     L  WRD +  V   LN
Sbjct: 183 LADEAVLAARDLEHIEVVGIHAHIGSQIFGTDPFIANADVCLDLLARWRDEHGIVLSELN 242

Query: 245 LGGGFGIRYTEDDEPLHATEYVEKIIEAVKENASRYGFDIPEIWIEPGRSLVGDAGTTLY 304
           LGGG GIRYT +D P+    Y + ++EAV++   R  F  P + +EPGR++VG +  TLY
Sbjct: 243 LGGGMGIRYTHEDHPVEVKRYGKAVLEAVEDACERLDFPRPRLIVEPGRAIVGPSTLTLY 302

Query: 305 TVGSQKEVPGVRQYVAVDGGMNDNIRPALYQAKYEAAAANRIGEAHDKTVSIAGKCCESG 364
            +G+ K +PG+  +V+VDGGM DNIRPALY A +E   ANR  EA  + V++ GK CESG
Sbjct: 303 EIGTIKPLPGLTTWVSVDGGMGDNIRPALYDAVHEVTLANRTSEAEPQAVTVVGKHCESG 362

Query: 365 DMLIWDIDLP-EVKEGDLLAVFCTGAYGYSMANNYNRIPRPAVVFVENGEAHLVVKRETY 423
           D++     LP ++  GDLLAV  TGAY  SMA+NYN +PRP  V V++G+A  +V+RET 
Sbjct: 363 DLVREHAPLPGDLAVGDLLAVAATGAYTASMASNYNLLPRPGAVLVKDGQARELVRRETL 422

Query: 424 EDIVKLDLPFK 434
           ED+V+ D+P +
Sbjct: 423 EDLVRRDVPIR 433


Lambda     K      H
   0.319    0.137    0.401 

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: 564
Number of extensions: 24
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: 439
Length of database: 433
Length adjustment: 32
Effective length of query: 407
Effective length of database: 401
Effective search space:   163207
Effective search space used:   163207
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: 51 (24.3 bits)

Align candidate WP_052666188.1 NITAL_RS10480 (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.1805.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-141  457.9   0.0   1.4e-141  457.7   0.0    1.0  1  lcl|NCBI__GCF_000969705.1:WP_052666188.1  NITAL_RS10480 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052666188.1  NITAL_RS10480 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.7   0.0  1.4e-141  1.4e-141       3     416 ..      11     429 ..       9     430 .. 0.98

  Alignments for each domain:
  == domain 1  score: 457.7 bits;  conditional E-value: 1.4e-141
                                 TIGR01048   3 ekkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllae 71 
                                               +++dg l i+g+++++la+ +gtPl+v+de++lrer++++ + f +    v+YA+KA+  + +l+l+++
  lcl|NCBI__GCF_000969705.1:WP_052666188.1  11 RDEDGVLHIGGAAVTDLARDHGTPLWVVDEADLRERCRRYVTGFPGV--DVAYASKAWCTVGLLQLVED 77 
                                               6899****************************************864..8******************* PP

                                 TIGR01048  72 eGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgk 140
                                               eGl +dv s+GEl +al Agv++ k++++gn+k ++el  al+++   i+vds++el++le++a+   +
  lcl|NCBI__GCF_000969705.1:WP_052666188.1  78 EGLLVDVASEGELHTALVAGVDPAKLIHHGNNKGDAELDLALKVGLGRIVVDSFDELDRLERLAAARDI 146
                                               ********************************************************************* PP

                                 TIGR01048 141 karvllRvnpdvdaktheyisTGlkesKFGieve..eaeeayelalkleslelvGihvHIGSqildlep 207
                                                a+v+lR++p++da+they+ TG+ + KFG++++   a ea+ +a +le++e+vGih+HIGSqi+ ++p
  lcl|NCBI__GCF_000969705.1:WP_052666188.1 147 VAQVWLRITPGIDAHTHEYVRTGHDDAKFGFTLSlgLADEAVLAARDLEHIEVVGIHAHIGSQIFGTDP 215
                                               ********************************9988999****************************** PP

                                 TIGR01048 208 fveaaekvvklleelkee.gieleeldlGGGlgisyeeeeeapdleeyaeklleklekea.elgl.klk 273
                                               f++ a+  ++ll+++++e gi l+el+lGGG+gi+y++e+++++++ y +++le++e+++ +l + +++
  lcl|NCBI__GCF_000969705.1:WP_052666188.1 216 FIANADVCLDLLARWRDEhGIVLSELNLGGGMGIRYTHEDHPVEVKRYGKAVLEAVEDACeRLDFpRPR 284
                                               ***************9999*****************************************999999*** PP

                                 TIGR01048 274 lilEpGRslvanagvlltrVesvKeves.rkfvlvDagmndliRpalYeayheiaalkrleeeetetvd 341
                                               li+EpGR++v++++ +l++++++K  +  +++v+vD+gm d+iRpalY+a+he+++++r++e+e + v+
  lcl|NCBI__GCF_000969705.1:WP_052666188.1 285 LIVEPGRAIVGPSTLTLYEIGTIKPLPGlTTWVSVDGGMGDNIRPALYDAVHEVTLANRTSEAEPQAVT 353
                                               *************************9988**************************************** PP

                                 TIGR01048 342 vvGplCEsgDvlakdrelp.eveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretl 409
                                               vvG++CEsgD++ +   lp +   Gdllava++GAY+asm+snYn  prp +vlv++g+ar ++rretl
  lcl|NCBI__GCF_000969705.1:WP_052666188.1 354 VVGKHCESGDLVREHAPLPgDLAVGDLLAVAATGAYTASMASNYNLLPRPGAVLVKDGQARELVRRETL 422
                                               *******************999*********************************************** PP

                                 TIGR01048 410 edllale 416
                                               edl++ +
  lcl|NCBI__GCF_000969705.1:WP_052666188.1 423 EDLVRRD 429
                                               ****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (433 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: 00:00:00.01
# Mc/sec: 10.64
//
[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