Alignments for a candidate for dapF in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapF in Stenotrophomonas chelatiphaga DSM 21508

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_057508891.1 ABB28_RS12205 diaminopimelate epimerase

Query= curated2:Q3BXU3
         (284 letters)



>NCBI__GCF_001431535.1:WP_057508891.1
          Length = 292

 Score =  428 bits (1100), Expect = e-125
 Identities = 204/278 (73%), Positives = 234/278 (84%)

Query: 6   RSGRLRFTKMHGAGNDFVVLDLRDGTPPPDAALAAQLADRHFGVGCDQILTIEAPRSEGA 65
           R   LRF+KMHGAGNDF+++DLRDGTPPP   LAA+LADRH GVGCDQI+TIE PRS  A
Sbjct: 14  RGAPLRFSKMHGAGNDFIMIDLRDGTPPPSPQLAARLADRHTGVGCDQIITIEPPRSATA 73

Query: 66  VAAYGIWNSDGSAARQCGNGARCVAAWLVRDGTAQGERFIIDSPMSAHAVERLDGDRYAV 125
           VA+Y IWNSDGS+++QCGNGARCVAAWLVR+G      F IDSP++ H V  L  D +AV
Sbjct: 74  VASYRIWNSDGSSSQQCGNGARCVAAWLVRNGDTADSEFAIDSPLATHPVRTLGEDHFAV 133

Query: 126 AMGVPQFEPAQIPLAGFAHARDEYALPVHGETVRFGAVSMGNPHAVVEVGRVDAAPVERV 185
            MGVP FEPAQIPL GFAH RDEY LPV GETVRFGAVSMGNPHAV+EVG VDAAPVER+
Sbjct: 134 EMGVPVFEPAQIPLIGFAHPRDEYLLPVQGETVRFGAVSMGNPHAVIEVGLVDAAPVERL 193

Query: 186 GALLQQNAAFPDSVNVGFVQVVDPAHVRLRVFERGVGETLACGSGACAAAVVLMQRGRVE 245
           GA LQQ+A+FP+SVNVGF QV++P H RLRV+ERGVGETLACGSGACAAAV LMQRGR+ 
Sbjct: 194 GASLQQHASFPESVNVGFAQVLEPDHARLRVYERGVGETLACGSGACAAAVSLMQRGRLG 253

Query: 246 RDVQVSLPGGELRIRWPGDQEQVVMSGPAVFVFDGEWN 283
            D ++SLPGGELRI+W G+ + VVMSGP+ FVF+GEWN
Sbjct: 254 PDARISLPGGELRIQWAGEGQPVVMSGPSAFVFEGEWN 291


Lambda     K      H
   0.321    0.137    0.423 

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: 354
Number of extensions: 11
Number of successful extensions: 1
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: 284
Length of database: 292
Length adjustment: 26
Effective length of query: 258
Effective length of database: 266
Effective search space:    68628
Effective search space used:    68628
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate WP_057508891.1 ABB28_RS12205 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

# 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/TIGR00652.hmm
# target sequence database:        /tmp/gapView.26325.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00652  [M=270]
Accession:   TIGR00652
Description: DapF: diaminopimelate epimerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.1e-78  250.3   0.0    1.3e-78  250.2   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057508891.1  ABB28_RS12205 diaminopimelate ep


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508891.1  ABB28_RS12205 diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.2   0.0   1.3e-78   1.3e-78       2     268 ..      19     290 ..      18     292 .] 0.96

  Alignments for each domain:
  == domain 1  score: 250.2 bits;  conditional E-value: 1.3e-78
                                 TIGR00652   2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSe 69 
                                               +F+kmhG+gNdF+++d +d + + + ++l+++++drhtgvg+D+++++ep  s +a + +ri+NsDGS+
  lcl|NCBI__GCF_001431535.1:WP_057508891.1  19 RFSKMHGAGNDFIMIDLRDGTPPPS-PQLAARLADRHTGVGCDQIITIEPpRSATAVASYRIWNSDGSS 86 
                                               8******************999999.9**********************978889999*********** PP

                                 TIGR00652  70 aemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeee 138
                                                ++CGNg+Rc+a++++ +g +  +e+ + +   +  v    e+ +  v+mg p f++++ipl +  + +
  lcl|NCBI__GCF_001431535.1:WP_057508891.1  87 SQQCGNGARCVAAWLVRNGDTADSEFAIDSPLATHPVRTLGED-HFAVEMGVPVFEPAQIPLIGFAHPR 154
                                               *********************99*******9999999999999.9******************999999 PP

                                 TIGR00652 139 keellalev..l...vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklr 202
                                               +e+ll ++   +   +v++GnPH+v+ v  v+ +++e+lg+ l++h +fpe vNv f++v+++d+ +lr
  lcl|NCBI__GCF_001431535.1:WP_057508891.1 155 DEYLLPVQGetVrfgAVSMGNPHAVIEVGLVDAAPVERLGASLQQHASFPESVNVGFAQVLEPDHARLR 223
                                               999998877663569****************************************************** PP

                                 TIGR00652 203 vyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegel 268
                                               vyERG+geTlaCG+Ga+A+av  ++ g++  ++++ l+ggeL i++  +g  v + Gp+ +v+ege 
  lcl|NCBI__GCF_001431535.1:WP_057508891.1 224 VYERGVGETLACGSGACAAAVSLMQRGRLGPDARISLPGGELRIQWAGEGqPVVMSGPSAFVFEGEW 290
                                               **************************************************99************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (292 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.87
//
[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