Alignments for a candidate for lysA in Nostoc punctiforme ATCC 29133; PCC 73102

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Nostoc punctiforme ATCC 29133; PCC 73102

Align diaminopimelate decarboxylase subunit (EC 4.1.1.20) (characterized)
to candidate WP_012412220.1 NPUN_RS30310 diaminopimelate decarboxylase

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



>NCBI__GCF_000020025.1:WP_012412220.1
          Length = 465

 Score =  383 bits (983), Expect = e-111
 Identities = 202/426 (47%), Positives = 281/426 (65%), Gaps = 6/426 (1%)

Query: 6   TSRQNQHGHLEIGGVDALYLAEKYGTPLYVYDVALIRERAKSFKQAFISAGL-KAQVAYA 64
           T+R + H  LEIGG D   L +++G+PLY+ D   +R   + ++ AF      ++QV YA
Sbjct: 37  TARVHNHDSLEIGGCDVTTLVKQFGSPLYILDEETLRSACQQYRDAFKQYYKGESQVLYA 96

Query: 65  SKAFSSVAMIQLAEEEGLSLDVVSGGELYTAVAAGFPAERIHFHGNNKSREELRMALEHR 124
           SKA++ +A+  +A  EGL +DVVSGGELYTA+ AG   E+I+ HGNNKSREEL +A+E  
Sbjct: 97  SKAWNCLAVCAIAASEGLGIDVVSGGELYTALQAGVSPEKIYLHGNNKSREELILAIESG 156

Query: 125 IGCIVVDNFYEIALLEDLCKETGHSIDVLLRITPGVEAHTHDYITTGQEDSKFGFDLHNG 184
           +  IV DN+YE+  L ++  + G SI ++LR+TPG+E HTH+YI TG  DSKFGFD ++ 
Sbjct: 157 V-TIVADNWYELRTLVEIA-QPGQSIRIMLRLTPGIECHTHEYIRTGHLDSKFGFDPND- 213

Query: 185 QTERAIEQVLQSEHIQLLGVHCHIGSQIFDTAGFVLAAEKIFKKLDEWRDSYSFVSKVLN 244
             +     V Q   +  +GVH HIGSQIF+       A  + + L +    Y      LN
Sbjct: 214 -LDEVFTFVSQQSTLDCVGVHAHIGSQIFERQPHQDLAAVMVQWLRD-AGKYGLNITELN 271

Query: 245 LGGGFGIRYTEDDEPLHATEYVEKIIEAVKENASRYGFDIPEIWIEPGRSLVGDAGTTLY 304
           +GGG GI+YTE D+P    E+V+ I E V+E  +     +P++  EPGRSL+  A  T Y
Sbjct: 272 VGGGLGIKYTESDDPPSIEEWVKAICEVVQEACAVENLPLPKLLSEPGRSLIATACVTAY 331

Query: 305 TVGSQKEVPGVRQYVAVDGGMNDNIRPALYQAKYEAAAANRIGEAHDKTVSIAGKCCESG 364
           TVGS K +P +R YVA+DGGM+DN RP  YQ+ Y A  AN++     +TV+IAGK CESG
Sbjct: 332 TVGSSKVIPEIRTYVAIDGGMSDNPRPITYQSVYRAVVANKMSSPVTQTVTIAGKHCESG 391

Query: 365 DMLIWDIDLPEVKEGDLLAVFCTGAYGYSMANNYNRIPRPAVVFVENGEAHLVVKRETYE 424
           D+LI +  LP+ + GD+L V  TGAY YSMA+NYNR+PRPA V V NGEA+L+++RETY+
Sbjct: 392 DILIKNALLPKTEPGDILVVMGTGAYNYSMASNYNRLPRPAAVVVANGEANLILQRETYQ 451

Query: 425 DIVKLD 430
           D+++ D
Sbjct: 452 DLIRQD 457


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: 533
Number of extensions: 23
Number of successful extensions: 5
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: 465
Length adjustment: 33
Effective length of query: 406
Effective length of database: 432
Effective search space:   175392
Effective search space used:   175392
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_012412220.1 NPUN_RS30310 (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.1378.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-156  506.1   0.0   3.4e-156  505.8   0.0    1.0  1  lcl|NCBI__GCF_000020025.1:WP_012412220.1  NPUN_RS30310 diaminopimelate dec


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020025.1:WP_012412220.1  NPUN_RS30310 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  505.8   0.0  3.4e-156  3.4e-156       5     416 ..      42     457 ..      38     458 .. 0.97

  Alignments for each domain:
  == domain 1  score: 505.8 bits;  conditional E-value: 3.4e-156
                                 TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafka...eeslvlYAvKAnsnlavlrlla 70 
                                               ++ +lei+g+d+++l+++fg+PlY++deetlr+++++++ afk+    es+vlYA+KA+++lav  ++a
  lcl|NCBI__GCF_000020025.1:WP_012412220.1  42 NHDSLEIGGCDVTTLVKQFGSPLYILDEETLRSACQQYRDAFKQyykGESQVLYASKAWNCLAVCAIAA 110
                                               56789**************************************9754445******************* PP

                                 TIGR01048  71 eeGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelg 139
                                               +eGlg+dvvsgGEl++al+Agv++eki+++gn+ks+eel  a+e++++ i++d++ el++l eia+   
  lcl|NCBI__GCF_000020025.1:WP_012412220.1 111 SEGLGIDVVSGGELYTALQAGVSPEKIYLHGNNKSREELILAIESGVT-IVADNWYELRTLVEIAQPG- 177
                                               ***********************************************8.****************976. PP

                                 TIGR01048 140 kkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepf 208
                                               +++r++lR++p+++++theyi TG+ +sKFG+++++  e++++++++++l++vG+h+HIGSqi++ +p+
  lcl|NCBI__GCF_000020025.1:WP_012412220.1 178 QSIRIMLRLTPGIECHTHEYIRTGHLDSKFGFDPNDLDEVFTFVSQQSTLDCVGVHAHIGSQIFERQPH 246
                                               ********************************************************************* PP

                                 TIGR01048 209 veaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekea.elgl.klkli 275
                                               ++ a+ +v++l++  + g++++el++GGGlgi+y+e++++p++ee+++++ e +++++   +l  +kl+
  lcl|NCBI__GCF_000020025.1:WP_012412220.1 247 QDLAAVMVQWLRDAGKYGLNITELNVGGGLGIKYTESDDPPSIEEWVKAICEVVQEACaVENLpLPKLL 315
                                               *************9999***************************************996556679**** PP

                                 TIGR01048 276 lEpGRslvanagvlltrVesvKeves.rkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvv 343
                                                EpGRsl+a+a+v+ ++V+s K  ++ r++v++D+gm+d+ Rp++Y+++++ +++++++   t+tv+++
  lcl|NCBI__GCF_000020025.1:WP_012412220.1 316 SEPGRSLIATACVTAYTVGSSKVIPEiRTYVAIDGGMSDNPRPITYQSVYRAVVANKMSSPVTQTVTIA 384
                                               ************************999****************************************** PP

                                 TIGR01048 344 GplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledl 412
                                               G++CEsgD+l+k+  lp++e+Gd+l+v+ +GAY++sm+snYn+ prpa+v+v +g+a+li++ret++dl
  lcl|NCBI__GCF_000020025.1:WP_012412220.1 385 GKHCESGDILIKNALLPKTEPGDILVVMGTGAYNYSMASNYNRLPRPAAVVVANGEANLILQRETYQDL 453
                                               ********************************************************************* PP

                                 TIGR01048 413 lale 416
                                               ++++
  lcl|NCBI__GCF_000020025.1:WP_012412220.1 454 IRQD 457
                                               *987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (465 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: 7.90
//
[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