Alignments for a candidate for dapE in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Azospirillum brasilense Sp245

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate AZOBR_RS03470 AZOBR_RS03470 succinyl-diaminopimelate desuccinylase

Query= BRENDA::P44514
         (377 letters)



>FitnessBrowser__azobra:AZOBR_RS03470
          Length = 397

 Score =  291 bits (746), Expect = 2e-83
 Identities = 164/380 (43%), Positives = 229/380 (60%), Gaps = 10/380 (2%)

Query: 6   VSLAQDLIRRPSISPNDEGCQQIIAERLEKLGFQIEWMPFND-----TLNLWAKHGTSEP 60
           V++AQ LIR PS++P D G   ++   L  LGF    + F +       NL+A+ GT  P
Sbjct: 16  VAVAQALIRCPSVTPEDGGALGVLEAALAPLGFVCHRLRFEEEGTAPVDNLYARLGTEGP 75

Query: 61  VIAFAGHTDVVPTGDENQWSSPPFSAEIIDGMLYGRGAADMKGSLAAMIVAAEEYVKA-- 118
              FAGHTDVVP G+   WS  PF+AEI +G LYGRGA DMKG++AA + AA  +VKA  
Sbjct: 76  NFCFAGHTDVVPPGELKGWSIDPFAAEIHNGRLYGRGAVDMKGAIAAFVAAAARHVKAVK 135

Query: 119 --NPNHKGTIALLITSDEEATAKDGTIHVVETLMARDEKITYCMVGEPSSAKNLGDVVKN 176
                 KG+I+LLIT DEE  A +GT  V++ L A+ EK+  C+VGEP++ K LGD++K 
Sbjct: 136 ETGDAPKGSISLLITGDEEGVAINGTRKVLDWLQAKGEKLDACVVGEPTNPKALGDMIKI 195

Query: 177 GRRGSITGNLYIQGIQGHVAYPHLAENPIHKAALFLQELTTYQWDKGNEFFPPTSLQIAN 236
           GRRGS+T  L + G QGHVAYPHLA+NP+ + A  L  +T    D G   F P++L++  
Sbjct: 196 GRRGSMTAFLTVHGAQGHVAYPHLADNPLPRLARMLTAITAEPLDAGTPHFQPSNLELTT 255

Query: 237 IHAGTGSNNVIPAELYIQFNLRYCTEVTDEIIKQKVAEMLEKHNLKYRIEWNLSGKPFLT 296
           I  G  ++NVIPA+     N+R+    T + +   + E L+     Y ++  +SG  FLT
Sbjct: 256 IDVGNPAHNVIPAQGKATLNIRFNDLHTADTLLAWLRERLDGVGGSYELDHFVSGDSFLT 315

Query: 297 KPGKLLDSITSAIEETIGITPKAETGGGTSDGRFIALMGAEVVEFGPLNSTIHKVNECVS 356
            PG L + +  A E   G  P+  T GGTSD RFI      VVEFG +  T+HKV+E  +
Sbjct: 316 PPGPLTELVADAAERVTGRRPEYSTTGGTSDARFIKNF-CPVVEFGLVGQTMHKVDEHTA 374

Query: 357 VEDLGKCGEIYHKMLVNLLD 376
           ++DL +  +IY ++L N+ D
Sbjct: 375 LDDLTRLTDIYGEVLRNVFD 394


Lambda     K      H
   0.316    0.134    0.394 

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: 447
Number of extensions: 25
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: 377
Length of database: 397
Length adjustment: 30
Effective length of query: 347
Effective length of database: 367
Effective search space:   127349
Effective search space used:   127349
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate AZOBR_RS03470 AZOBR_RS03470 (succinyl-diaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

# 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/TIGR01246.hmm
# target sequence database:        /tmp/gapView.4107.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01246  [M=370]
Accession:   TIGR01246
Description: dapE_proteo: succinyl-diaminopimelate desuccinylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-130  420.4   0.0   3.4e-130  420.3   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS03470  AZOBR_RS03470 succinyl-diaminopi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS03470  AZOBR_RS03470 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.3   0.0  3.4e-130  3.4e-130       3     369 ..      17     391 ..      15     392 .. 0.96

  Alignments for each domain:
  == domain 1  score: 420.3 bits;  conditional E-value: 3.4e-130
                                 TIGR01246   3 elakeLisrksvtPndagaqeliaerLkklgfeieilefed.....tknlwatrgteepvlvfaGhtDv 66 
                                               ++a+ Li+ +svtP+d ga+ ++++ L  lgf +++l+fe+     + nl+a+ gte p+++faGhtDv
  lcl|FitnessBrowser__azobra:AZOBR_RS03470  17 AVAQALIRCPSVTPEDGGALGVLEAALAPLGFVCHRLRFEEegtapVDNLYARLGTEGPNFCFAGHTDV 85 
                                               57899*********************************9874444468999****************** PP

                                 TIGR01246  67 vPaGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadh....kGslsllitsDee 131
                                               vP Gel+ Ws dpf++e+++G+lygrGa+Dmkg++aafv+aa r+vk+  +     kGs+sllit Dee
  lcl|FitnessBrowser__azobra:AZOBR_RS03470  86 VPPGELKGWSIDPFAAEIHNGRLYGRGAVDMKGAIAAFVAAAARHVKAVKETgdapKGSISLLITGDEE 154
                                               *********************************************987655333359************ PP

                                 TIGR01246 132 geaidGtkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenP 200
                                               g ai+Gt+kv+++l+++ e++d +vvgeP+  k+lGD+ikiGrrGs+t+ l+++G qGhvaYPh+a+nP
  lcl|FitnessBrowser__azobra:AZOBR_RS03470 155 GVAINGTRKVLDWLQAKGEKLDACVVGEPTNPKALGDMIKIGRRGSMTAFLTVHGAQGHVAYPHLADNP 223
                                               ********************************************************************* PP

                                 TIGR01246 201 vhkavpvlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskve 269
                                               +++++++l++++a+ lD G+ +f+ps+l+++ i++g+ a nviP++ k++ n+rf+  +++++l   ++
  lcl|FitnessBrowser__azobra:AZOBR_RS03470 224 LPRLARMLTAITAEPLDAGTPHFQPSNLELTTIDVGNPAHNVIPAQGKATLNIRFNDLHTADTLLAWLR 292
                                               ********************************************************************* PP

                                 TIGR01246 270 kildkhkldYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelG 338
                                               + ld  +  Yel++ +sg++flt  g l++ va+a e+v++++pe st+GGtsDarfi+++ + vve+G
  lcl|FitnessBrowser__azobra:AZOBR_RS03470 293 ERLDGVGGSYELDHFVSGDSFLTPPGPLTELVADAAERVTGRRPEYSTTGGTSDARFIKNF-CPVVEFG 360
                                               *************************************************************.******* PP

                                 TIGR01246 339 lvndtihkvneavkiedleklsevyekllee 369
                                               lv +t+hkv+e++ ++dl +l+++y ++l++
  lcl|FitnessBrowser__azobra:AZOBR_RS03470 361 LVGQTMHKVDEHTALDDLTRLTDIYGEVLRN 391
                                               ***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (397 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: 10.94
//
[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