Alignments for a candidate for lysA in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Synechococcus elongatus PCC 7942

Align diaminopimelate decarboxylase subunit (EC 4.1.1.20) (characterized)
to candidate Synpcc7942_0262 Synpcc7942_0262 diaminopimelate decarboxylase

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



>FitnessBrowser__SynE:Synpcc7942_0262
          Length = 464

 Score =  364 bits (935), Expect = e-105
 Identities = 196/433 (45%), Positives = 274/433 (63%), Gaps = 19/433 (4%)

Query: 6   TSRQNQHGHLEIGGVDALYLAEKYGTPLYVYDVALIRERAKSFKQAFISAGLKAQVA-YA 64
           T+     G LE+GG     L E+YG+PLY+ D   +R   +S++ A       A +  YA
Sbjct: 35  TASVTADGQLEVGGCRVSDLVERYGSPLYILDEQTLRAACQSYRSALAHHYPGAALPIYA 94

Query: 65  SKAFSSVAMIQLAEEEGLSLDVVSGGELYTAVAAGFPAERIHFHGNNKSREELRMALEHR 124
           SKA++ +A+  L  +EGL +DVVS GELYTA+ AG P++R++FHGNNKS  EL M +E  
Sbjct: 95  SKAWNCLAVCALVAQEGLGIDVVSAGELYTALQAGVPSDRLYFHGNNKSLSELAMGVE-- 152

Query: 125 IGC-IVVDNFYEIALLEDLCKETGHSIDVLLRITPGVEAHTHDYITTGQEDSKFGFDLHN 183
            GC IVVDN+ E+  LE +  E    + V++R TPG+E HTH+YI TG  DSKFGFD   
Sbjct: 153 AGCTIVVDNWQELRNLEAIAAEQQREVRVMIRFTPGIECHTHEYIRTGHLDSKFGFD--P 210

Query: 184 GQTERAIEQVLQSEHIQLLGVHCHIGSQIF------DTAGFVLAAEKIFKKLDEWRDSYS 237
            Q +  +  ++   +++ +G+H HIGSQIF      D AG ++ A    K L     +  
Sbjct: 211 DQLDALLAALVDQPYLRCIGLHAHIGSQIFELQPHADLAGVLVGAYA--KAL-----ALG 263

Query: 238 FVSKVLNLGGGFGIRYTEDDEPLHATEYVEKIIEAVKENASRYGFDIPEIWIEPGRSLVG 297
                LN+GGG GIRYTE D+P    E+V ++ E++          +P++  EPGRSL+G
Sbjct: 264 LPIAELNVGGGLGIRYTESDDPPSIDEWVRQVSESLVAACQAADLPLPKLICEPGRSLIG 323

Query: 298 DAGTTLYTVGSQKEVPGVRQYVAVDGGMNDNIRPALYQAKYEAAAANRIGEAHDKTVSIA 357
            A  T Y +GS+KEVPG+R Y+AVDGGM+DN RP  YQ+ Y A  ANR+  +  +TV++A
Sbjct: 324 TACVTAYQIGSRKEVPGIRTYLAVDGGMSDNPRPITYQSTYRAVIANRLNVSDRETVTVA 383

Query: 358 GKCCESGDMLIWDIDLPEVKEGDLLAVFCTGAYGYSMANNYNRIPRPAVVFVENGEAHLV 417
           GK CESGD+L+ D +L   + GD+L V  TGAY YSMA+NYNRI RPA V V NGEA ++
Sbjct: 384 GKHCESGDVLLKDAELAPSQPGDILVVLATGAYNYSMASNYNRIARPAAVLVNNGEAQII 443

Query: 418 VKRETYEDIVKLD 430
           + RE+ +D+++ D
Sbjct: 444 LARESLQDLLRQD 456


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: 510
Number of extensions: 17
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: 464
Length adjustment: 33
Effective length of query: 406
Effective length of database: 431
Effective search space:   174986
Effective search space used:   174986
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 Synpcc7942_0262 Synpcc7942_0262 (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.23699.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.3e-149  481.7   0.0   8.3e-149  481.5   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_0262  Synpcc7942_0262 diaminopimelate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_0262  Synpcc7942_0262 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  481.5   0.0  8.3e-149  8.3e-149       4     416 ..      39     456 ..      36     457 .. 0.97

  Alignments for each domain:
  == domain 1  score: 481.5 bits;  conditional E-value: 8.3e-149
                                 TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafka...eeslvlYAvKAnsnlavlrll 69 
                                               + dg+le++g+++ +l+e++g+PlY++de+tlr++++++++a ++     +l +YA+KA+++lav  l+
  lcl|FitnessBrowser__SynE:Synpcc7942_0262  39 TADGQLEVGGCRVSDLVERYGSPLYILDEQTLRAACQSYRSALAHhypGAALPIYASKAWNCLAVCALV 107
                                               6799**************************************9986533449***************** PP

                                 TIGR01048  70 aeeGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakel 138
                                               a+eGlg+dvvs GEl++al+Agv++++++f+gn+ks +el++ +e++++ i+vd+++el+ le+ia+e+
  lcl|FitnessBrowser__SynE:Synpcc7942_0262 108 AQEGLGIDVVSAGELYTALQAGVPSDRLYFHGNNKSLSELAMGVEAGCT-IVVDNWQELRNLEAIAAEQ 175
                                               ************************************************8.******************* PP

                                 TIGR01048 139 gkkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlep 207
                                                 ++rv++R +p+++++theyi TG+ +sKFG+++++  +   + +++++l+++G+h+HIGSqi++l+p
  lcl|FitnessBrowser__SynE:Synpcc7942_0262 176 QREVRVMIRFTPGIECHTHEYIRTGHLDSKFGFDPDQLDALLAALVDQPYLRCIGLHAHIGSQIFELQP 244
                                               ************************************9999999************************** PP

                                 TIGR01048 208 fveaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekea.elgl.klkl 274
                                               + + a  +v ++++  + g+ ++el++GGGlgi+y+e++++p+++e+++++ e+l  ++ +  l  +kl
  lcl|FitnessBrowser__SynE:Synpcc7942_0262 245 HADLAGVLVGAYAKALALGLPIAELNVGGGLGIRYTESDDPPSIDEWVRQVSESLVAACqAADLpLPKL 313
                                               **************999****************************************997667789*** PP

                                 TIGR01048 275 ilEpGRslvanagvlltrVesvKeves.rkfvlvDagmndliRpalYeayheiaalkrleeeetetvdv 342
                                               i+EpGRsl+++a+v+ ++++s+Kev+  r++ +vD+gm+d+ Rp++Y++ ++ + ++rl+   +etv+v
  lcl|FitnessBrowser__SynE:Synpcc7942_0262 314 ICEPGRSLIGTACVTAYQIGSRKEVPGiRTYLAVDGGMSDNPRPITYQSTYRAVIANRLNVSDRETVTV 382
                                               *************************989***************************************** PP

                                 TIGR01048 343 vGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretled 411
                                               +G++CEsgDvl kd el   ++Gd+l+v ++GAY++sm+snYn+++rpa+vlv++g+a++i+ re+l+d
  lcl|FitnessBrowser__SynE:Synpcc7942_0262 383 AGKHCESGDVLLKDAELAPSQPGDILVVLATGAYNYSMASNYNRIARPAAVLVNNGEAQIILARESLQD 451
                                               ********************************************************************* PP

                                 TIGR01048 412 llale 416
                                               ll+++
  lcl|FitnessBrowser__SynE:Synpcc7942_0262 452 LLRQD 456
                                               **987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (464 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: 7.24
//
[ok]

This GapMind analysis is from Apr 09 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