Alignments for a candidate for lysA in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Dyella japonica UNC79MFTsu3.2

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate N515DRAFT_2124 N515DRAFT_2124 diaminopimelate decarboxylase

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



>FitnessBrowser__Dyella79:N515DRAFT_2124
          Length = 426

 Score =  339 bits (869), Expect = 1e-97
 Identities = 182/401 (45%), Positives = 252/401 (62%), Gaps = 2/401 (0%)

Query: 14  ENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSVHLAFAIKANPNLAVLGVLA 73
           + V +  +A  + TP + YS   +    + L+ AL G  ++ L +A+KAN NLA+L ++A
Sbjct: 19  DGVDLRRLAERIPTPFHAYSANAIRTRIAGLQQALHGFDAL-LCYAVKANSNLAILQLMA 77

Query: 74  RQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGIGQFNLELEEEGEV 133
             G GAD+VS GEL RAL AG+PA+ +VFSGVGKT AE+   L  GI +FN+E  +E E+
Sbjct: 78  EAGVGADIVSSGELWRALHAGIPAQRIVFSGVGKTAAEIAEALAAGILRFNVESADELEL 137

Query: 134 LADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRALEIFDRLAKRPGLN 193
           L  +A      A A +R+NPDVDA THAKISTGKAENKFGV+ID A   F   A++  + 
Sbjct: 138 LQRMAAELHVVAHAAVRINPDVDAQTHAKISTGKAENKFGVSIDEARRWFADSARQANVR 197

Query: 194 LRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLGGGLGVPYHAGQTVST 253
           L G+ +HIGSQ+  + P   A+ RV     +L AAGH I  +D+GGGLGV Y  GQ    
Sbjct: 198 LDGLHVHIGSQILSVEPFRLAFARVAAFWRELEAAGHAIASIDVGGGLGVRYRDGQVPIP 257

Query: 254 AEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAAGNPYVIVDAAMNDLA 313
             ++ A +     G+   L+ EPGR++   AGVL+T V+ VK      ++++DAAMNDL 
Sbjct: 258 PGDYAAAIREALAGFRGRLLLEPGRYLVAEAGVLLTRVVRVKHGERRRFLVLDAAMNDLL 317

Query: 314 RPALYDAYHEF-EAVEPTGEKFVANIAGPVCETGDTFAMGREIDVVKSGDLAVFRTAGAY 372
           RP+LYDA+H+    ++        ++ GPVCETGDTFA+ RE+  + +G+L + RT GAY
Sbjct: 318 RPSLYDAWHDIVPLLDDARPPHRYDVVGPVCETGDTFAVERELPELHAGELVLIRTTGAY 377

Query: 373 GATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAER 413
           GA MASTYNSR L  EVL+   R A+V  R   E ++  E+
Sbjct: 378 GAAMASTYNSRPLAAEVLLDRGRHAIVRRRQSLEDMVAGEQ 418


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: 525
Number of extensions: 20
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: 426
Length adjustment: 32
Effective length of query: 387
Effective length of database: 394
Effective search space:   152478
Effective search space used:   152478
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 N515DRAFT_2124 N515DRAFT_2124 (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.18869.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     4e-146  472.7   0.0   4.9e-146  472.4   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2124  N515DRAFT_2124 diaminopimelate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2124  N515DRAFT_2124 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.4   0.0  4.9e-146  4.9e-146      11     416 ..      18     417 ..      11     418 .. 0.98

  Alignments for each domain:
  == domain 1  score: 472.4 bits;  conditional E-value: 4.9e-146
                                    TIGR01048  11 iegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgl 76 
                                                   +gvdl++lae+  tP++ y+++++r r++ l++a ++ ++l++YAvKAnsnla+l+l+ae+G+g+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2124  18 FDGVDLRRLAERIPTPFHAYSANAIRTRIAGLQQALHGFDALLCYAVKANSNLAILQLMAEAGVGA 83 
                                                  6899**********************************999************************* PP

                                    TIGR01048  77 dvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkka 142
                                                  d+vs GEl ral+Ag++a++ivfsg+gk+ +e+++al+++i  +nv+s +elell+++a+el   a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2124  84 DIVSSGELWRALHAGIPAQRIVFSGVGKTAAEIAEALAAGILRFNVESADELELLQRMAAELHVVA 149
                                                  ****************************************************************** PP

                                    TIGR01048 143 rvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepf 208
                                                  + ++R+npdvda+th +isTG++e+KFG++++ea++ +   +++++++l G+hvHIGSqil +epf
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2124 150 HAAVRINPDVDAQTHAKISTGKAENKFGVSIDEARRWFADSARQANVRLDGLHVHIGSQILSVEPF 215
                                                  ****************************************************************** PP

                                    TIGR01048 209 veaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklkl 274
                                                  + a+++v+ + +el+++g  ++ +d+GGGlg++y++ + ++ + +ya+++ e+l++     ++ +l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2124 216 RLAFARVAAFWRELEAAGHAIASIDVGGGLGVRYRDGQVPIPPGDYAAAIREALAG-----FRGRL 276
                                                  ***************************************************99999.....89*** PP

                                    TIGR01048 275 ilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetv 340
                                                  +lEpGR+lva+agvlltrV  vK+ e r+f + Da+mndl+Rp+lY+a+h+i++l + ++++ +++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2124 277 LLEPGRYLVAEAGVLLTRVVRVKHGERRRFLVLDAAMNDLLRPSLYDAWHDIVPLLD-DARPPHRY 341
                                                  *******************************************************55.8999**** PP

                                    TIGR01048 341 dvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrr 406
                                                  dvvGp+CE+gD++a +relpe ++G+l++++ +GAYga+m+s+Ynsrp +aevl++ g+  ++rrr
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2124 342 DVVGPVCETGDTFAVERELPELHAGELVLIRTTGAYGAAMASTYNSRPLAAEVLLDRGRHAIVRRR 407
                                                  ****************************************************************** PP

                                    TIGR01048 407 etledllale 416
                                                  ++led++a e
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2124 408 QSLEDMVAGE 417
                                                  ******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (426 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.38
//
[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