Alignments for a candidate for dapE in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Hydrogenophaga taeniospiralis NBRC 102512

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate WP_068169213.1 HTA01S_RS08380 succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>NCBI__GCF_001592305.1:WP_068169213.1
          Length = 390

 Score =  429 bits (1102), Expect = e-125
 Identities = 221/381 (58%), Positives = 268/381 (70%), Gaps = 9/381 (2%)

Query: 4   TQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTK----NIWLRRGT- 58
           T +L L +ELI+R SVTP D  CQ  LA RL  +GFA E L  G       N+W RRG  
Sbjct: 2   TATLRLTEELIARASVTPLDAGCQAQLASRLSALGFACETLESGPADFRVTNLWARRGRG 61

Query: 59  KAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVA 118
             P + FAGHTDVVPTGP+E W S PF P+ RDG+LYGRGA+DMK S+A  V ACE F+A
Sbjct: 62  DQPTLVFAGHTDVVPTGPLEAWASDPFVPSHRDGKLYGRGASDMKASLAAMVVACEEFIA 121

Query: 119 KHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNG 178
            +P     IA L+TSDEEG A DGT  V   L+ R E +D+CIVGEPT+V++ GDMIKNG
Sbjct: 122 SNPAPGIDIAFLLTSDEEGPANDGTVIVCRELQRRGERLDWCIVGEPTSVERTGDMIKNG 181

Query: 179 RRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNI 238
           RRG++SG LTVKG QGHIAYP LA NP+H  APAL EL   VWD GN +FPPTS+QISNI
Sbjct: 182 RRGTMSGKLTVKGIQGHIAYPQLARNPIHMVAPALAELVATVWDAGNAFFPPTSWQISNI 241

Query: 239 NGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQ----YDLQWSCSGQP 294
           +GGTGA+NVIPG + + FNFRFST ST  GL+QRV  IL + G++    +DL W+  G P
Sbjct: 242 HGGTGASNVIPGTVVIDFNFRFSTASTPEGLQQRVADILQRQGLRACTDFDLDWTVGGLP 301

Query: 295 FLTQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINE 354
           FLT+ G L D  RAAI    GI+ +LSTTGGTSDGRFI  +  ++IELGP NATIH+I+E
Sbjct: 302 FLTEPGPLVDAVRAAIRAETGIDTQLSTTGGTSDGRFIAQVCPQVIELGPPNATIHKIDE 361

Query: 355 NVRLNDIPKLSAVYEGILARL 375
           +V + DI  L  +Y   L +L
Sbjct: 362 HVAVADIEPLKNIYRRTLDQL 382


Lambda     K      H
   0.317    0.135    0.400 

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: 481
Number of extensions: 17
Number of successful extensions: 3
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: 381
Length of database: 390
Length adjustment: 30
Effective length of query: 351
Effective length of database: 360
Effective search space:   126360
Effective search space used:   126360
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 WP_068169213.1 HTA01S_RS08380 (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.13045.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-149  482.7   0.0   4.2e-149  482.5   0.0    1.0  1  lcl|NCBI__GCF_001592305.1:WP_068169213.1  HTA01S_RS08380 succinyl-diaminop


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068169213.1  HTA01S_RS08380 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.5   0.0  4.2e-149  4.2e-149       3     370 .]       6     382 ..       4     382 .. 0.97

  Alignments for each domain:
  == domain 1  score: 482.5 bits;  conditional E-value: 4.2e-149
                                 TIGR01246   3 elakeLisrksvtPndagaqeliaerLkklgfeieilefe....dtknlwatrgt.eepvlvfaGhtDv 66 
                                                l++eLi r svtP dag+q+ +a+rL++lgf++e+le +     ++nlwa+rg  ++p+lvfaGhtDv
  lcl|NCBI__GCF_001592305.1:WP_068169213.1   6 RLTEELIARASVTPLDAGCQAQLASRLSALGFACETLESGpadfRVTNLWARRGRgDQPTLVFAGHTDV 74 
                                               6899*********************************9984433479*******9889*********** PP

                                 TIGR01246  67 vPaGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeai 135
                                               vP+G+le+W sdpf p++rdGklygrGa Dmk+slaa+vva+e+f+++n+     +++l+tsDeeg a 
  lcl|NCBI__GCF_001592305.1:WP_068169213.1  75 VPTGPLEAWASDPFVPSHRDGKLYGRGASDMKASLAAMVVACEEFIASNPAPGIDIAFLLTSDEEGPAN 143
                                               **************************************************9877*************** PP

                                 TIGR01246 136 dGtkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhka 204
                                               dGt+ v   l+ r e +d+++vgeP+sv++ GD+ik+GrrG ++gkl++kGiqGh+aYP++a+nP+h +
  lcl|NCBI__GCF_001592305.1:WP_068169213.1 144 DGTVIVCRELQRRGERLDWCIVGEPTSVERTGDMIKNGRRGTMSGKLTVKGIQGHIAYPQLARNPIHMV 212
                                               ********************************************************************* PP

                                 TIGR01246 205 vpvlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekild 273
                                               +p+l+el+a+ +D Gn+ffpp+s qi+ni++gtgasnviPg + + fn+rfs+ ++ e l+++v++il+
  lcl|NCBI__GCF_001592305.1:WP_068169213.1 213 APALAELVATVWDAGNAFFPPTSWQISNIHGGTGASNVIPGTVVIDFNFRFSTASTPEGLQQRVADILQ 281
                                               ********************************************************************* PP

                                 TIGR01246 274 khkl....dYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelG 338
                                               +++l    d++l+w++ g pflt+ g l+++v++ai+  +++ ++lst+GGtsD+rfia++  +v+elG
  lcl|NCBI__GCF_001592305.1:WP_068169213.1 282 RQGLractDFDLDWTVGGLPFLTEPGPLVDAVRAAIRAETGIDTQLSTTGGTSDGRFIAQVCPQVIELG 350
                                               *96544449************************************************************ PP

                                 TIGR01246 339 lvndtihkvneavkiedleklsevyeklleel 370
                                               + n+tihk++e+v ++d+e l+++y+++l +l
  lcl|NCBI__GCF_001592305.1:WP_068169213.1 351 PPNATIHKIDEHVAVADIEPLKNIYRRTLDQL 382
                                               **************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (390 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: 10.66
//
[ok]

This GapMind analysis is from Apr 10 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