Alignments for a candidate for lysA in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Bacteroides thetaiotaomicron VPI-5482

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate 350902 BT1374 diaminopimelate decarboxylase (NCBI ptt file)

Query= reanno::Btheta:350902
         (386 letters)



>FitnessBrowser__Btheta:350902
          Length = 386

 Score =  773 bits (1997), Expect = 0.0
 Identities = 386/386 (100%), Positives = 386/386 (100%)

Query: 1   MKGIFPIDKFRTLQTPFYYYDTKVLRDTLSAINQEVAKYPSYSVHYAVKANANPKVLTII 60
           MKGIFPIDKFRTLQTPFYYYDTKVLRDTLSAINQEVAKYPSYSVHYAVKANANPKVLTII
Sbjct: 1   MKGIFPIDKFRTLQTPFYYYDTKVLRDTLSAINQEVAKYPSYSVHYAVKANANPKVLTII 60

Query: 61  RESGMGADCVSGGEIRAAVRAGFPANKIVFAGVGKADWEINLGLEYGIFCFNVESIPELE 120
           RESGMGADCVSGGEIRAAVRAGFPANKIVFAGVGKADWEINLGLEYGIFCFNVESIPELE
Sbjct: 61  RESGMGADCVSGGEIRAAVRAGFPANKIVFAGVGKADWEINLGLEYGIFCFNVESIPELE 120

Query: 121 VINELAAAQNKIANVAFRINPDVGAHTHANITTGLAENKFGISMQDMDRVIDVALEMKNV 180
           VINELAAAQNKIANVAFRINPDVGAHTHANITTGLAENKFGISMQDMDRVIDVALEMKNV
Sbjct: 121 VINELAAAQNKIANVAFRINPDVGAHTHANITTGLAENKFGISMQDMDRVIDVALEMKNV 180

Query: 181 KFIGLHFHIGSQILDMGDFIALCNRVNELQDKLEARRILVEHINVGGGLGIDYGHPNRQS 240
           KFIGLHFHIGSQILDMGDFIALCNRVNELQDKLEARRILVEHINVGGGLGIDYGHPNRQS
Sbjct: 181 KFIGLHFHIGSQILDMGDFIALCNRVNELQDKLEARRILVEHINVGGGLGIDYGHPNRQS 240

Query: 241 VPDFKSYFATYAGQLKLRPYQTLHFELGRAVVGQCGSLISKVLYVKQGTKKKFAILDAGM 300
           VPDFKSYFATYAGQLKLRPYQTLHFELGRAVVGQCGSLISKVLYVKQGTKKKFAILDAGM
Sbjct: 241 VPDFKSYFATYAGQLKLRPYQTLHFELGRAVVGQCGSLISKVLYVKQGTKKKFAILDAGM 300

Query: 301 TDLIRPALYQAYHKMENITSEEPVEAYDVVGPICESSDVFGKAIDLNKVKRGDLIALRSA 360
           TDLIRPALYQAYHKMENITSEEPVEAYDVVGPICESSDVFGKAIDLNKVKRGDLIALRSA
Sbjct: 301 TDLIRPALYQAYHKMENITSEEPVEAYDVVGPICESSDVFGKAIDLNKVKRGDLIALRSA 360

Query: 361 GAYGEIMASGYNCRELPKGYTSDELV 386
           GAYGEIMASGYNCRELPKGYTSDELV
Sbjct: 361 GAYGEIMASGYNCRELPKGYTSDELV 386


Lambda     K      H
   0.321    0.138    0.405 

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: 634
Number of extensions: 19
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: 386
Length of database: 386
Length adjustment: 30
Effective length of query: 356
Effective length of database: 356
Effective search space:   126736
Effective search space used:   126736
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: 50 (23.9 bits)

Align candidate 350902 BT1374 (diaminopimelate decarboxylase (NCBI ptt file))
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.1422.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   7.7e-126  405.9   0.1     1e-125  405.5   0.1    1.0  1  lcl|FitnessBrowser__Btheta:350902  BT1374 diaminopimelate decarboxy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350902  BT1374 diaminopimelate decarboxylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.5   0.1    1e-125    1e-125      22     390 ..      12     377 ..       7     382 .. 0.95

  Alignments for each domain:
  == domain 1  score: 405.5 bits;  conditional E-value: 1e-125
                          TIGR01048  22 efgtPlYvydeetlrerlealkeafkaees.lvlYAvKAnsnlavlrllaeeGlgldvvsgGEleralaAgvkaek 96 
                                        +  tP+Y yd++ lr  l+a+++ ++++ s  v+YAvKAn+n +vl +++e G+g+d+vsgGE+ +a+ Ag++a+k
  lcl|FitnessBrowser__Btheta:350902  12 TLQTPFYYYDTKVLRDTLSAINQEVAKYPSySVHYAVKANANPKVLTIIRESGMGADCVSGGEIRAAVRAGFPANK 87 
                                        568**********************997777********************************************* PP

                          TIGR01048  97 ivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdaktheyisTGlkesKFGie 172
                                        ivf+g+gk + e++  le++i ++nv+s+ ele ++e+a+ ++k a+v++R+npdv+a+th  i+TGl+e+KFGi+
  lcl|FitnessBrowser__Btheta:350902  88 IVFAGVGKADWEINLGLEYGIFCFNVESIPELEVINELAAAQNKIANVAFRINPDVGAHTHANITTGLAENKFGIS 163
                                        **************************************************************************** PP

                          TIGR01048 173 veeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGGGlgisyeeee.. 246
                                        +++  +++ +al++++++ +G+h+HIGSqild+ +f++ +++v +l ++l+++ i +e++++GGGlgi+y + +  
  lcl|FitnessBrowser__Btheta:350902 164 MQDMDRVIDVALEMKNVKFIGLHFHIGSQILDMGDFIALCNRVNELQDKLEARRILVEHINVGGGLGIDYGHPNrq 239
                                        **********************************************************************876511 PP

                          TIGR01048 247 eapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYea 322
                                        + pd ++y ++ + +l+       +++l +E GR++v++ g l+ +V +vK+  ++kf++ Dagm+dliRpalY+a
  lcl|FitnessBrowser__Btheta:350902 240 SVPDFKSYFATYAGQLKL----RPYQTLHFELGRAVVGQCGSLISKVLYVKQGTKKKFAILDAGMTDLIRPALYQA 311
                                        456666666666666655....589*************************************************** PP

                          TIGR01048 323 yheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprp 390
                                        yh++ ++  ++ee+ e +dvvGp+CEs+Dv++k ++l++v++Gdl+a++saGAYg  m+s Yn r  p
  lcl|FitnessBrowser__Btheta:350902 312 YHKMENI--TSEEPVEAYDVVGPICESSDVFGKAIDLNKVKRGDLIALRSAGAYGEIMASGYNCRELP 377
                                        *******..7899**************************************************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (386 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: 9.47
//
[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