Alignments for a candidate for lysA in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Desulfovibrio vulgaris Hildenborough

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate 208063 DVU2566 diaminopimelate decarboxylase

Query= curated2:O27390
         (428 letters)



>MicrobesOnline__882:208063
          Length = 421

 Score =  291 bits (745), Expect = 3e-83
 Identities = 173/408 (42%), Positives = 242/408 (59%), Gaps = 17/408 (4%)

Query: 16  GGADAVELADEYGTPLYVIDEMRIRENYRRLYRAFSGEYSRFQVFYACKANTNLAVMRIL 75
           G     EL + YG+PLYV  E  +R+  R + +A S  +  F+V Y+ KAN+NLA++ I+
Sbjct: 16  GLTSPTELVETYGSPLYVYSEAILRQRCREM-KALSS-HPGFRVNYSAKANSNLALLHII 73

Query: 76  EEEGSGIDAVSPGEIYTALMAGFDPDRILYTGNNVRDDELQFALDSGVRINVDSRSQLLR 135
            EEG  +DA+SPGE++  L AGF PD+ILY  NNV  +EL  A+  G+ ++VDS SQL  
Sbjct: 74  REEGLVVDAMSPGELFMNLRAGFSPDKILYVCNNVSAEELGNAVSHGLLVSVDSLSQLDL 133

Query: 136 LSEIAPEGLRISFRVNPLVGAGHHEHCITGGEMSKFGVMEREAPEVYRMAMDLGFEPVGI 195
             E+ P G R+  R NP +GAGHH+  +T G+ +KFGV      EV  +         GI
Sbjct: 134 YGEVNPGG-RVMVRFNPGIGAGHHKKVVTAGKETKFGVDPASIDEVRTILARHNLTLAGI 192

Query: 196 HAHIGSGILDPEPFMLAVETLMDIAGRVHEATGVEFEFIDFGGGLGIPYTP-EEEP-LDI 253
           + HIGS  L+PE ++ A   L+ +A R  +      E IDFGGG GIPY   + +P LD+
Sbjct: 193 NQHIGSLFLEPESYVEAARFLLTLAERFDDV-----EVIDFGGGFGIPYHKYDNQPRLDL 247

Query: 254 DEFASKITGLFKDKLSEYGLGRPMMCLEPGRYIVGDASYLLTRVNTIKES-YRKFAGVDA 312
               ++   L        G  R    +EPGRY+V +   LL  V+++K +   ++ G D 
Sbjct: 248 TAMGAQFDDLISGWAQRRGY-RGRFLVEPGRYVVAECGLLLGSVHSVKSNGANRYVGTDL 306

Query: 313 GFNTLLRPAMYGSYHHILVAERPLDEPSEKM---DVAGNVCESGDLFARDRQLPEINEGD 369
           GFN L RP MY ++H I V  R    PS+ +    V GN+CESGD+ AR+R LP + EGD
Sbjct: 307 GFNVLARPVMYDAHHDIEV-YREDGAPSDLLLPQTVVGNICESGDIIARNRPLPPVEEGD 365

Query: 370 VLAIMNAGAYSFSMSSQYNSRPRPAEVLV-REGKVDVVRERETFSDLL 416
           +L +++AGAY + MSS YN R RPAEVL+  EG+  +VR RET  DL+
Sbjct: 366 ILGVLDAGAYGYVMSSSYNQRMRPAEVLIDLEGRPRLVRRRETLDDLV 413


Lambda     K      H
   0.320    0.140    0.408 

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: 577
Number of extensions: 30
Number of successful extensions: 8
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: 428
Length of database: 421
Length adjustment: 32
Effective length of query: 396
Effective length of database: 389
Effective search space:   154044
Effective search space used:   154044
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate 208063 DVU2566 (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.18629.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   8.2e-116  372.8   0.0   1.1e-115  372.4   0.0    1.0  1  lcl|MicrobesOnline__882:208063  DVU2566 diaminopimelate decarbox


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208063  DVU2566 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.4   0.0  1.1e-115  1.1e-115      16     414 ..      20     414 ..       9     416 .. 0.94

  Alignments for each domain:
  == domain 1  score: 372.4 bits;  conditional E-value: 1.1e-115
                       TIGR01048  16 lkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgGEleralaAgvka 94 
                                      +el+e++g+PlYvy+e+ lr+r++++k+  ++   +v Y +KAnsnla+l++++eeGl +d++s GEl + l Ag+++
  lcl|MicrobesOnline__882:208063  20 PTELVETYGSPLYVYSEAILRQRCREMKALSSHPGFRVNYSAKANSNLALLHIIREEGLVVDAMSPGELFMNLRAGFSP 98 
                                     579*************************99998878******************************************* PP

                       TIGR01048  95 ekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdaktheyisTGlkesKFGiev 173
                                     +ki++  n++s eel +a++++   ++vds+++l+l  e++++     rv++R np+++a +h+++ T+ ke KFG+++
  lcl|MicrobesOnline__882:208063  99 DKILYVCNNVSAEELGNAVSHGLL-VSVDSLSQLDLYGEVNPGG----RVMVRFNPGIGAGHHKKVVTAGKETKFGVDP 172
                                     ***********************7.*******************....******************************* PP

                       TIGR01048 174 eeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdl. 251
                                     +   + ++++l++++l+l Gi+ HIGS  l+ e +veaa+ +++l+e+      ++e++d+GGG+gi+y++ +++p+l 
  lcl|MicrobesOnline__882:208063 173 A-SIDEVRTILARHNLTLAGINQHIGSLFLEPESYVEAARFLLTLAER----FDDVEVIDFGGGFGIPYHKYDNQPRLd 246
                                     *.8899999***************************************....5899**************998887651 PP

                       TIGR01048 252 .eeyaeklleklekea.elglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaa 328
                                      + + +++ + +++ a + g + + ++EpGR++va+ g ll +V+svK+++  ++v  D g+n l Rp++Y+a h+i +
  lcl|MicrobesOnline__882:208063 247 lTAMGAQFDDLISGWAqRRGYRGRFLVEPGRYVVAECGLLLGSVHSVKSNGANRYVGTDLGFNVLARPVMYDAHHDIEV 325
                                     156667778888888889999********************************************************** PP

                       TIGR01048 329 lkrleeeet..etvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlve.egkarlir 404
                                      ++  + ++     +vvG++CEsgD++a++r lp veeGd+l v +aGAYg+ mss Yn+r rpaevl++ eg+ rl+r
  lcl|MicrobesOnline__882:208063 326 YREDGAPSDllLPQTVVGNICESGDIIARNRPLPPVEEGDILGVLDAGAYGYVMSSSYNQRMRPAEVLIDlEGRPRLVR 404
                                     *77444433115679******************************************************95679***** PP

                       TIGR01048 405 rretledlla 414
                                     rretl+dl+a
  lcl|MicrobesOnline__882:208063 405 RRETLDDLVA 414
                                     ********97 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.44
//
[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