Aligments for a candidate for lysA in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Aligments for a candidate for lysA in Caulobacter crescentus NA1000

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate CCNA_02296 CCNA_02296 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>lcl|FitnessBrowser__Caulo:CCNA_02296 CCNA_02296 diaminopimelate
           decarboxylase
          Length = 421

 Score =  295 bits (754), Expect = 2e-84
 Identities = 160/387 (41%), Positives = 244/387 (63%), Gaps = 7/387 (1%)

Query: 13  TPFYLYDFDKIKQAFLNYKEAFKGR---KSLICYALKANSNLSILSLLAHLESGADCVSI 69
           TP Y+Y    +++ F+ +++A         LI YA+KANSN+++L +L  L +GAD VS 
Sbjct: 27  TPVYVYSRATLERHFVVFRDALAMSGVVDPLIAYAVKANSNVAVLKVLGDLGAGADTVSE 86

Query: 70  GEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIK 129
           GE++RAL AGI   RIVFSGVGK+  EI  AL+  +  +NVES  EL  I  +A  LG++
Sbjct: 87  GEVRRALAAGIPGERIVFSGVGKARREIAFALQAGVAEINVESEPELNLIAEVAAELGVR 146

Query: 130 ARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQ 189
           A+++ R+NP++ A  H  I+TG  ENKFGV   EA  ++  A  +A L+PV V  HIGSQ
Sbjct: 147 AKVAFRVNPDVAAGGHAKIATGKSENKFGVSFAEAARLYANASNNANLQPVGVACHIGSQ 206

Query: 190 LLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENE-ETIKLYDYAQGILNA 248
           + DL P+  A  K+  + + L+A G+ +   D+GGG+GV Y N  E     ++A  +   
Sbjct: 207 ITDLAPMRAAFTKMRGLVEQLLAEGLSVERLDLGGGLGVPYFNHPEPPSPAEFAAMVGEV 266

Query: 249 LQGLDLTIICEPGRSIVAESGELITQVLY-EKKAQNKRFVIVDAGMNDFLRPSLYHAKHA 307
            QGL +T+  EPGR I A +G L+++V++  ++ + ++F+++DA MND +RP++Y A H 
Sbjct: 267 TQGLPVTLAFEPGRVIAANAGVLVSEVIHVHERPEGRKFLVIDAAMNDLVRPAMYDAFHD 326

Query: 308 IRVITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQYN 367
           IR +    G  +   DVVGPVCE+ DTF +D  LP    GD +A    GAYG++MAS+YN
Sbjct: 327 IRPVIQRTGETV--YDVVGPVCETGDTFTRDRALPPFAAGDLVAFMSAGAYGAAMASEYN 384

Query: 368 SRPKLLELALEDHKIRVIRKREALEDL 394
           +RP + E+ ++  +  VIR+R   +++
Sbjct: 385 TRPLVPEVLVDGDRYAVIRQRPTYDEM 411


Lambda     K      H
   0.319    0.138    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: 355
Number of extensions: 13
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: 405
Length of database: 421
Length adjustment: 31
Effective length of query: 374
Effective length of database: 390
Effective search space:   145860
Effective search space used:   145860
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: 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.27838.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: 00:00:00.01
# Mc/sec: 9.82
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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