Aligments for a candidate for lysA in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Aligments for a candidate for lysA in Herbaspirillum seropedicae SmR1

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate HSERO_RS00950 HSERO_RS00950 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>FitnessBrowser__HerbieS:HSERO_RS00950
          Length = 430

 Score =  310 bits (793), Expect = 7e-89
 Identities = 169/403 (41%), Positives = 249/403 (61%), Gaps = 18/403 (4%)

Query: 13  TPFYLYDFDKIKQAFLNYKEAFK--GRK------SLICYALKANSNLSILSLLAHLESGA 64
           TP Y+Y    + + F  Y  A +  GR       +L+CY++K+NSNL++L+LL  L SG 
Sbjct: 27  TPLYVYSKAALVENFSAYANACQQAGRADGGKGGALVCYSVKSNSNLAVLNLLGRLGSGF 86

Query: 65  DCVSIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQ 124
           D VS GE+ R + AG    +++FSGVGK   E++ AL+ +IL  NVES  E+  +  +A 
Sbjct: 87  DIVSGGELLRVVAAGGDARKVIFSGVGKGRDEMKLALEHDILCFNVESIPEVARLNEVAG 146

Query: 125 SLGIKARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHF 184
           +LG +ARIS+R+NPN+DAKTHPYISTGLKENKFGV  ++AL  +  A     +E V +  
Sbjct: 147 ALGKRARISLRVNPNVDAKTHPYISTGLKENKFGVAYEDALNCYRAAAALPHIEVVGIDC 206

Query: 185 HIGSQLLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQG 244
           HIGSQLLD  P++EA  K+  +  +L A GI +   D+GGGIG+ Y++E+ + + DY   
Sbjct: 207 HIGSQLLDDSPLLEALDKIIDMVDALEAEGIPIHHLDIGGGIGIRYDDEQPVAIGDYLAR 266

Query: 245 IL--------NALQGLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDF 296
           +         +  QG  + ++ EPGRS+V  +G L+T+V Y K  + K F +VDA MND 
Sbjct: 267 VFARVDAWRASKYQGRPIQVMFEPGRSVVGNAGLLLTEVQYLKHGEGKNFAVVDAAMNDL 326

Query: 297 LRPSLYHAKHAIRVITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVG 356
           +RP++Y A H ++ +  + G+     DVVGPVCES D   +   L  +  GD +A+   G
Sbjct: 327 MRPAMYEAWHGVKTVKENAGQP-RIYDVVGPVCESGDWLARSREL-AIGEGDLLALMSAG 384

Query: 357 AYGSSMASQYNSRPKLLELALEDHKIRVIRKREALEDLWRLEE 399
           AYG +MAS YN+R +  E+ ++  +  +IR RE   DL+ LE+
Sbjct: 385 AYGMTMASNYNTRGRAAEVLVDGERAHLIRARENPADLFALEK 427


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: 404
Number of extensions: 21
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: 430
Length adjustment: 32
Effective length of query: 373
Effective length of database: 398
Effective search space:   148454
Effective search space used:   148454
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 HSERO_RS00950 HSERO_RS00950 (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.3448.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   6.5e-158  511.5   0.0   8.1e-158  511.2   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS00950  HSERO_RS00950 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS00950  HSERO_RS00950 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.2   0.0  8.1e-158  8.1e-158       5     416 ..       7     426 ..       4     427 .. 0.95

  Alignments for each domain:
  == domain 1  score: 511.2 bits;  conditional E-value: 8.1e-158
                                  TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafka...ees......lvlYAvKAnsnl 63 
                                                ++g l +e+v+l++lae+fgtPlYvy++++l e+++a+++a ++   +        lv+Y vK+nsnl
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950   7 RNGVLHAEQVSLATLAEQFGTPLYVYSKAALVENFSAYANACQQagrA-DggkggaLVCYSVKSNSNL 73 
                                                7899**********************************9999875541.13445679*********** PP

                                  TIGR01048  64 avlrllaeeGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelell 131
                                                avl+ll ++G+g+d+vsgGEl r++aAg +a k++fsg+gk ++e++ ale++i ++nv+s+ e+++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950  74 AVLNLLGRLGSGFDIVSGGELLRVVAAGGDARKVIFSGVGKGRDEMKLALEHDILCFNVESIPEVARL 141
                                                ******************************************************************** PP

                                  TIGR01048 132 eeiakelgkkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIG 199
                                                +e+a+ lgk+ar++lRvnp+vdakth+yisTGlke+KFG+++e+a++ y++a++l+++e+vGi++HIG
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950 142 NEVAGALGKRARISLRVNPNVDAKTHPYISTGLKENKFGVAYEDALNCYRAAAALPHIEVVGIDCHIG 209
                                                ******************************************************************** PP

                                  TIGR01048 200 SqildlepfveaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekea. 266
                                                Sq+ld +p+ ea++k++++++ l++egi +++ld+GGG+gi+y++e+ ++ + +y + + +++     
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950 210 SQLLDDSPLLEALDKIIDMVDALEAEGIPIHHLDIGGGIGIRYDDEQ-PVAIGDYLARVFARVDAWRa 276
                                                ********************************************999.*******9999998876433 PP

                                  TIGR01048 267 ..elglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrl 332
                                                   +g+  ++++EpGRs+v+nag llt+V+++K+ e ++f++vDa+mndl+Rpa+Yea+h + ++k+ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950 277 skYQGRPIQVMFEPGRSVVGNAGLLLTEVQYLKHGEGKNFAVVDAAMNDLMRPAMYEAWHGVKTVKE- 343
                                                3356779**********************************************************66. PP

                                  TIGR01048 333 eeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegka 400
                                                ++ +   +dvvGp+CEsgD la+ rel   e Gdlla++saGAYg++m+snYn+r+r+aevlv++++a
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950 344 NAGQPRIYDVVGPVCESGDWLARSRELAIGE-GDLLALMSAGAYGMTMASNYNTRGRAAEVLVDGERA 410
                                                88889**********************9888.************************************ PP

                                  TIGR01048 401 rlirrretledllale 416
                                                +lir re+ +dl+ale
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950 411 HLIRARENPADLFALE 426
                                                *************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (430 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: 00:00:00.02
# Mc/sec: 7.69
//
[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