GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Phaeobacter inhibens BS107

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate GFF336 PGA1_c03470 diaminopimelate decarboxylase LysA

Query= reanno::Korea:Ga0059261_2051
         (419 letters)



>FitnessBrowser__Phaeo:GFF336
          Length = 421

 Score =  421 bits (1082), Expect = e-122
 Identities = 221/422 (52%), Positives = 293/422 (69%), Gaps = 5/422 (1%)

Query: 1   MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSVHLAFAI 60
           MDHF  ++G L+AE+V +  IAA VGTP Y+YSTATL RH +   +AL G+  + + +A+
Sbjct: 1   MDHFLYRDGALYAEDVPVAEIAATVGTPFYLYSTATLLRHFNLFDDALKGMDHL-VCYAM 59

Query: 61  KANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGI 120
           KA  N A+L  LA+ G G DVVS GE  RA AAG+P + +VFSGVGKT+ E++  L  GI
Sbjct: 60  KAASNQAILKTLAQAGAGMDVVSQGEYLRAKAAGVPGDRIVFSGVGKTQDEIRTALSGGI 119

Query: 121 GQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRAL 180
            QFN+E E E +V+  +A   G  AP  +RVNPDVDA THAKI+TGK+ENKFG+ I RA 
Sbjct: 120 RQFNVESEPEMDVINAVALELGVVAPITVRVNPDVDAKTHAKIATGKSENKFGIPIARAR 179

Query: 181 EIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLGGG 240
           E++ R A  PGL + G+ +HIGSQLTELAP E AY++V EL  QLRA GH I  +DLGGG
Sbjct: 180 EVYARAASLPGLKVIGIDVHIGSQLTELAPFELAYQKVAELTEQLRADGHDIHRLDLGGG 239

Query: 241 LGVPY-HAGQTVSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAAG 299
           LG+PY  +  T     E+GAMV R        +  EPGR I GNAG++V++VI+VK    
Sbjct: 240 LGIPYTRSNDTPPLPVEYGAMVQRTLGHLGCEIEIEPGRLIAGNAGIMVSKVIYVKSGED 299

Query: 300 NPYVIVDAAMNDLARPALYDAYHEF-EAVEPTG--EKFVANIAGPVCETGDTFAMGREID 356
             ++I+D AMNDL RPA+Y+AYH+    +EP+   E+   +I GPVCETGDTFA  R++ 
Sbjct: 300 RDFLIIDGAMNDLIRPAMYEAYHDIVPVIEPSAGVEQRAYDIVGPVCETGDTFARHRDMP 359

Query: 357 VVKSGDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVPE 416
            +++GDL  FR+AGAYGA MAS YNSR L+PEVLV+GD+FAV+  R   + ++  + +PE
Sbjct: 360 PLEAGDLVAFRSAGAYGAVMASEYNSRPLIPEVLVNGDQFAVIRRRPDFDEMINRDTIPE 419

Query: 417 WV 418
           W+
Sbjct: 420 WL 421


Lambda     K      H
   0.318    0.135    0.389 

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: 537
Number of extensions: 24
Number of successful extensions: 4
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: 419
Length of database: 421
Length adjustment: 32
Effective length of query: 387
Effective length of database: 389
Effective search space:   150543
Effective search space used:   150543
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF336 PGA1_c03470 (diaminopimelate decarboxylase LysA)
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.30901.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.8e-147  476.5   0.0   3.3e-147  476.3   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF336  PGA1_c03470 diaminopimelate deca


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF336  PGA1_c03470 diaminopimelate decarboxylase LysA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.3   0.0  3.3e-147  3.3e-147       5     416 ..       7     415 ..       4     416 .. 0.95

  Alignments for each domain:
  == domain 1  score: 476.3 bits;  conditional E-value: 3.3e-147
                         TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsg 81 
                                       +dg l++e+v+++e+a++ gtP+Y+y+++tl ++++ ++ a k+ ++lv+YA+KA sn a+l++la++G+g+dvvs+
  lcl|FitnessBrowser__Phaeo:GFF336   7 RDGALYAEDVPVAEIAATVGTPFYLYSTATLLRHFNLFDDALKGMDHLVCYAMKAASNQAILKTLAQAGAGMDVVSQ 83 
                                       6899************************************************************************* PP

                         TIGR01048  82 GEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakthe 158
                                       GE  ra+aAgv+ ++ivfsg+gk+++e+++al+ +i+ +nv+s+ e++ ++++a elg  a++++Rvnpdvdakth 
  lcl|FitnessBrowser__Phaeo:GFF336  84 GEYLRAKAAGVPGDRIVFSGVGKTQDEIRTALSGGIRQFNVESEPEMDVINAVALELGVVAPITVRVNPDVDAKTHA 160
                                       ***************************************************************************** PP

                         TIGR01048 159 yisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlG 235
                                       +i+TG+ e+KFGi +++a+e+y +a++l+ l+++Gi+vHIGSq+++l+pf+ a +kv++l+e+l+++g +++ ldlG
  lcl|FitnessBrowser__Phaeo:GFF336 161 KIATGKSENKFGIPIARAREVYARAASLPGLKVIGIDVHIGSQLTELAPFELAYQKVAELTEQLRADGHDIHRLDLG 237
                                       ***************************************************************************** PP

                         TIGR01048 236 GGlgisyeeeeeapdle.eyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagm 311
                                       GGlgi+y++++++p l  ey +++ ++l +     l  ++ +EpGR +++nag+++ +V +vK+ e r f ++D++m
  lcl|FitnessBrowser__Phaeo:GFF336 238 GGLGIPYTRSNDTPPLPvEYGAMVQRTLGH-----LGCEIEIEPGRLIAGNAGIMVSKVIYVKSGEDRDFLIIDGAM 309
                                       ********9988776651555555444444.....6899************************************** PP

                         TIGR01048 312 ndliRpalYeayheiaalkrlee.eetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsr 387
                                       ndliRpa+Yeayh+i+++ + ++  e+  +d+vGp+CE+gD++a+ r++p  e+Gdl+a +saGAYga m+s+Ynsr
  lcl|FitnessBrowser__Phaeo:GFF336 310 NDLIRPAMYEAYHDIVPVIEPSAgVEQRAYDIVGPVCETGDTFARHRDMPPLEAGDLVAFRSAGAYGAVMASEYNSR 386
                                       ****************99886651567889*********************************************** PP

                         TIGR01048 388 prpaevlveegkarlirrretledllale 416
                                       p + evlv++++  +irrr  ++++++ +
  lcl|FitnessBrowser__Phaeo:GFF336 387 PLIPEVLVNGDQFAVIRRRPDFDEMINRD 415
                                       ***********************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (421 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: 10.45
//
[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:

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:

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:

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:

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