Alignments for a candidate for lysA in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Caulobacter crescentus NA1000

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate CCNA_02296 CCNA_02296 diaminopimelate decarboxylase

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



>FitnessBrowser__Caulo:CCNA_02296
          Length = 421

 Score =  402 bits (1032), Expect = e-116
 Identities = 219/422 (51%), Positives = 280/422 (66%), Gaps = 5/422 (1%)

Query: 1   MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALA--GLPSVHLAF 58
           M+HF      L  E V +  IAAEVGTPVYVYS ATLERH    ++ALA  G+    +A+
Sbjct: 1   MNHFEYGPQGLACEGVPLAKIAAEVGTPVYVYSRATLERHFVVFRDALAMSGVVDPLIAY 60

Query: 59  AIKANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDE 118
           A+KAN N+AVL VL   G GAD VS GE++RALAAG+P E +VFSGVGK R E+   L  
Sbjct: 61  AVKANSNVAVLKVLGDLGAGADTVSEGEVRRALAAGIPGERIVFSGVGKARREIAFALQA 120

Query: 119 GIGQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDR 178
           G+ + N+E E E  ++A++A   G  A    RVNPDV AG HAKI+TGK+ENKFGV+   
Sbjct: 121 GVAEINVESEPELNLIAEVAAELGVRAKVAFRVNPDVAAGGHAKIATGKSENKFGVSFAE 180

Query: 179 ALEIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLG 238
           A  ++   +    L   GVA HIGSQ+T+LAP+ AA+ ++  LV QL A G ++  +DLG
Sbjct: 181 AARLYANASNNANLQPVGVACHIGSQITDLAPMRAAFTKMRGLVEQLLAEGLSVERLDLG 240

Query: 239 GGLGVPYHAGQTVSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWV-KPA 297
           GGLGVPY       +  EF AMV  VTQG  VTL FEPGR I  NAGVLV+EVI V +  
Sbjct: 241 GGLGVPYFNHPEPPSPAEFAAMVGEVTQGLPVTLAFEPGRVIAANAGVLVSEVIHVHERP 300

Query: 298 AGNPYVIVDAAMNDLARPALYDAYHEFE-AVEPTGEKFVANIAGPVCETGDTFAMGREID 356
            G  ++++DAAMNDL RPA+YDA+H+    ++ TGE  V ++ GPVCETGDTF   R + 
Sbjct: 301 EGRKFLVIDAAMNDLVRPAMYDAFHDIRPVIQRTGET-VYDVVGPVCETGDTFTRDRALP 359

Query: 357 VVKSGDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVPE 416
              +GDL  F +AGAYGA MAS YN+R LVPEVLV GDR+AV+  R   + ++  + VP+
Sbjct: 360 PFAAGDLVAFMSAGAYGAAMASEYNTRPLVPEVLVDGDRYAVIRQRPTYDEMLARDLVPD 419

Query: 417 WV 418
           WV
Sbjct: 420 WV 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: 551
Number of extensions: 21
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: 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 CCNA_02296 CCNA_02296 (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.32074.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-143  462.9   0.0   4.5e-143  462.6   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02296  CCNA_02296 diaminopimelate decar


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02296  CCNA_02296 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.6   0.0  4.5e-143  4.5e-143       9     416 ..      11     415 ..       6     416 .. 0.97

  Alignments for each domain:
  == domain 1  score: 462.6 bits;  conditional E-value: 4.5e-143
                             TIGR01048   9 leiegvdlkelaeefgtPlYvydeetlrerlealkeafka...ees.lvlYAvKAnsnlavlrllaeeGlgld 77 
                                           l +egv+l+++a+e gtP+Yvy+++tl++++  ++ a +        l++YAvKAnsn+avl++l ++G+g+d
  lcl|FitnessBrowser__Caulo:CCNA_02296  11 LACEGVPLAKIAAEVGTPVYVYSRATLERHFVVFRDALAMsgvV-DpLIAYAVKANSNVAVLKVLGDLGAGAD 82 
                                           7899********************************99874433.26************************** PP

                             TIGR01048  78 vvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnp 150
                                            vs+GE+ ralaAg++ e+ivfsg+gk ++e++ al++++  inv+s+ el+l+ e+a+elg +a+v++Rvnp
  lcl|FitnessBrowser__Caulo:CCNA_02296  83 TVSEGEVRRALAAGIPGERIVFSGVGKARREIAFALQAGVAEINVESEPELNLIAEVAAELGVRAKVAFRVNP 155
                                           ************************************************************************* PP

                             TIGR01048 151 dvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelk 223
                                           dv a  h +i+TG+ e+KFG++++ea++ y  a+++++l++vG+ +HIGSqi+dl+p+++a+ k+  l+e+l 
  lcl|FitnessBrowser__Caulo:CCNA_02296 156 DVAAGGHAKIATGKSENKFGVSFAEAARLYANASNNANLQPVGVACHIGSQITDLAPMRAAFTKMRGLVEQLL 228
                                           ************************************************************************* PP

                             TIGR01048 224 eegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesv 296
                                           +eg+++e ldlGGGlg++y ++ e+p+++e+a+++ e  +     gl ++l +EpGR ++anagvl+ +V +v
  lcl|FitnessBrowser__Caulo:CCNA_02296 229 AEGLSVERLDLGGGLGVPYFNHPEPPSPAEFAAMVGEVTQ-----GLPVTLAFEPGRVIAANAGVLVSEVIHV 296
                                           ********************************99885444.....59************************** PP

                             TIGR01048 297 Keves.rkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdll 368
                                            e+++ rkf ++Da+mndl+Rpa+Y+a h+i+++  ++ + ++++dvvGp+CE+gD++++dr+lp   +Gdl+
  lcl|FitnessBrowser__Caulo:CCNA_02296 297 HERPEgRKFLVIDAAMNDLVRPAMYDAFHDIRPV--IQRTGETVYDVVGPVCETGDTFTRDRALPPFAAGDLV 367
                                           **9989****************************..6677789****************************** PP

                             TIGR01048 369 avasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                           a +saGAYga+m+s+Yn+rp + evlv+++++ +ir+r t++++la +
  lcl|FitnessBrowser__Caulo:CCNA_02296 368 AFMSAGAYGAAMASEYNTRPLVPEVLVDGDRYAVIRQRPTYDEMLARD 415
                                           ********************************************9986 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: 00:00:00.02
# Mc/sec: 7.26
//
[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