Alignments for a candidate for lysA in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Azospirillum brasilense Sp245

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate AZOBR_RS16945 AZOBR_RS16945 diaminopimelate decarboxylase

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



>FitnessBrowser__azobra:AZOBR_RS16945
          Length = 421

 Score =  413 bits (1061), Expect = e-120
 Identities = 215/422 (50%), Positives = 283/422 (67%), Gaps = 5/422 (1%)

Query: 1   MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSVHLAFAI 60
           M  F  +NGV+HAE+V +  IAAEVGTP Y YSTA LE H SA   A AG     + +A+
Sbjct: 1   MSAFAYRNGVMHAESVPLSTIAAEVGTPFYCYSTAALEAHYSAYAGAFAG-QDADVCYAV 59

Query: 61  KANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGI 120
           KAN NLAV+   AR G GADVVSGGE++RALA G+PA  ++FSGVGKTR E++  L+ GI
Sbjct: 60  KANSNLAVIRAFARLGAGADVVSGGEMRRALAGGIPAGKIIFSGVGKTREEMRAALEAGI 119

Query: 121 GQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRAL 180
            Q N+E   E E L+++A + G TAP   RVNPDVDA THAKI+TGK ENKFGV  D A 
Sbjct: 120 HQINVESIPEVEALSEVAVSLGVTAPIAFRVNPDVDAKTHAKIATGKKENKFGVDYDHAR 179

Query: 181 EIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLGGG 240
           E++ + AK PG+    +A+HIGSQLT+LAP  AAY+RV  L+  LR  GH IT +DLGGG
Sbjct: 180 EVYAQAAKLPGIKPVAIAVHIGSQLTDLAPFRAAYERVAALLHVLREDGHDITRLDLGGG 239

Query: 241 LGVPYHAGQTVSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAAGN 300
           LG+ Y        A ++ AMV  +T      +  EPGR + GNAG+LV+ VI++K     
Sbjct: 240 LGIVYKHEAPPDIA-DYAAMVKSITGNLGCRISLEPGRSLVGNAGILVSRVIYLKQGLHR 298

Query: 301 PYVIVDAAMNDLARPALYDAYHEFEAVEPTGEKFVA---NIAGPVCETGDTFAMGREIDV 357
            +VI+DAAMNDL RP LY+AYH    V    +       ++ GPVCE+GDTFA+ R +  
Sbjct: 299 RFVIIDAAMNDLIRPTLYEAYHGIVPVTEPAKGAATEPYDVVGPVCESGDTFALQRALPA 358

Query: 358 VKSGDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVPEW 417
           +   +L    +AGAYGA M+STYN+R L+PEVLV+GD+F+V+  R+  E ++  +RVP+W
Sbjct: 359 MAPDELVAILSAGAYGAVMSSTYNTRPLIPEVLVNGDQFSVIRPRVSVEELLALDRVPDW 418

Query: 418 VR 419
           ++
Sbjct: 419 LK 420


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: 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: 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 AZOBR_RS16945 AZOBR_RS16945 (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.16944.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.1e-151  488.8   0.0   6.3e-151  488.5   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS16945  AZOBR_RS16945 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS16945  AZOBR_RS16945 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.5   0.0  6.3e-151  6.3e-151       5     416 ..       7     413 ..       4     414 .. 0.98

  Alignments for each domain:
  == domain 1  score: 488.5 bits;  conditional E-value: 6.3e-151
                                 TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeG 73 
                                               ++g + +e v+l ++a+e gtP+Y y++++l+++++a++ af+++++ v+YAvKAnsnlav+r +a++G
  lcl|FitnessBrowser__azobra:AZOBR_RS16945   7 RNGVMHAESVPLSTIAAEVGTPFYCYSTAALEAHYSAYAGAFAGQDADVCYAVKANSNLAVIRAFARLG 75 
                                               68999***************************************999********************** PP

                                 TIGR01048  74 lgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkka 142
                                               +g+dvvsgGE+ rala g++a ki+fsg+gk++ee++aale++i+ inv+s+ e+e l+e+a +lg +a
  lcl|FitnessBrowser__azobra:AZOBR_RS16945  76 AGADVVSGGEMRRALAGGIPAGKIIFSGVGKTREEMRAALEAGIHQINVESIPEVEALSEVAVSLGVTA 144
                                               ********************************************************************* PP

                                 TIGR01048 143 rvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfvea 211
                                               ++++Rvnpdvdakth +i+TG+ke+KFG+++++a+e+y +a+kl+ +++v i vHIGSq++dl+pf++a
  lcl|FitnessBrowser__azobra:AZOBR_RS16945 145 PIAFRVNPDVDAKTHAKIATGKKENKFGVDYDHAREVYAQAAKLPGIKPVAIAVHIGSQLTDLAPFRAA 213
                                               ********************************************************************* PP

                                 TIGR01048 212 aekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGR 280
                                                e+v+ ll+ l+e+g +++ ldlGGGlgi y++e  +pd+++ya++++ ++++    +l  ++ lEpGR
  lcl|FitnessBrowser__azobra:AZOBR_RS16945 214 YERVAALLHVLREDGHDITRLDLGGGLGIVYKHEA-PPDIADYAAMVK-SITG----NLGCRISLEPGR 276
                                               *********************************99.********9976.5555....3899******** PP

                                 TIGR01048 281 slvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkr.leeeetetvdvvGplCE 348
                                               slv+nag+l+ rV ++K+  +r+fv++Da+mndliRp lYeayh i+++++  + ++te +dvvGp+CE
  lcl|FitnessBrowser__azobra:AZOBR_RS16945 277 SLVGNAGILVSRVIYLKQGLHRRFVIIDAAMNDLIRPTLYEAYHGIVPVTEpAKGAATEPYDVVGPVCE 345
                                               ************************************************9984677899*********** PP

                                 TIGR01048 349 sgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                               sgD++a +r+lp++ +++l+a+ saGAYga mss+Yn+rp + evlv++++ ++ir r ++e+llal+
  lcl|FitnessBrowser__azobra:AZOBR_RS16945 346 SGDTFALQRALPAMAPDELVAILSAGAYGAVMSSTYNTRPLIPEVLVNGDQFSVIRPRVSVEELLALD 413
                                               *****************************************************************986 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: 11.27
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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