Alignments for a candidate for lysA in Phaeobacter inhibens BS107

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.6886.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: 11.51
//
[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