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

GapMind for Amino acid biosynthesis

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

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate 353244 BT3718 gamma-glutamyl phosphate reductase (NCBI ptt file)

Query= BRENDA::A7Y114
         (420 letters)



>FitnessBrowser__Btheta:353244
          Length = 417

 Score =  323 bits (829), Expect = 5e-93
 Identities = 185/420 (44%), Positives = 251/420 (59%), Gaps = 13/420 (3%)

Query: 7   NVNVEAQAIEAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGF 66
           N+N    A++A  AS+ L +LSD   N  L+ +AD    +   IL+ NEKDL    +   
Sbjct: 4   NLNGTFAAVQA--ASRELALLSDDTINQILNAVADATIAETSFILSENEKDLARMDK--- 58

Query: 67  TEAFMDRLSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMI 126
           +    DRL L++ER++  A   R+VA L  P G+ L + +  NG+++ KV+VP GVIG+I
Sbjct: 59  SNPKYDRLKLTEERLKGIAADTRNVATLPSPLGRILKETSRPNGMKLTKVSVPFGVIGII 118

Query: 127 YEARPNVTVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIAS 186
           YEARPNV+ D   L LKSGNA +LKGGS A +SN+AI+ VIHK L +  +    V+ + +
Sbjct: 119 YEARPNVSFDVFSLCLKSGNACILKGGSDADDSNRAIISVIHKVLEKFHVNPHIVELLPA 178

Query: 187 TDRAATNQLFTMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKA 246
            DR AT  L     +VD++IPRG   LI  V ENA +PV+ETG G CH Y D+  D  K 
Sbjct: 179 -DREATAALLNATGYVDLIIPRGSSNLINFVRENARIPVIETGAGICHTYFDEFGDTRKG 237

Query: 247 ISILVNAKTDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAV 306
             I+ NAKT R +VCNA +  I+H+  L      L   LK+  + ++ D      +    
Sbjct: 238 ADIIHNAKTRRVSVCNALDCTIIHEKRLGD-LPALCDQLKESKVTIYADTQAYQALEGYY 296

Query: 307 PAG------EDDWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFL 360
           PA        + +  E+L   +AVK V    DA+ HI+   ++HSE IVTEN+E A  F 
Sbjct: 297 PAELLQPATPESFGTEFLDYKMAVKTVKSFEDALGHIQENSSRHSECIVTENKERATLFT 356

Query: 361 AIVDAAAIYHNASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420
            IVDAA +Y N ST FTDG   G GAEIGISTQKLHARGPMGL  +T+ K++++G GQ R
Sbjct: 357 KIVDAACVYTNVSTAFTDGAQFGLGAEIGISTQKLHARGPMGLEEITSYKWVIEGDGQTR 416


Lambda     K      H
   0.315    0.131    0.365 

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: 441
Number of extensions: 18
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: 420
Length of database: 417
Length adjustment: 32
Effective length of query: 388
Effective length of database: 385
Effective search space:   149380
Effective search space used:   149380
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: 42 (22.0 bits)
S2: 50 (23.9 bits)

Align candidate 353244 BT3718 (gamma-glutamyl phosphate reductase (NCBI ptt file))
to HMM TIGR00407 (proA: glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41))

# 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/TIGR00407.hmm
# target sequence database:        /tmp/gapView.31311.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00407  [M=398]
Accession:   TIGR00407
Description: proA: glutamate-5-semialdehyde dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   6.9e-131  422.6   0.1   7.8e-131  422.5   0.1    1.0  1  lcl|FitnessBrowser__Btheta:353244  BT3718 gamma-glutamyl phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353244  BT3718 gamma-glutamyl phosphate reductase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.5   0.1  7.8e-131  7.8e-131       3     398 .]      14     406 ..      11     406 .. 0.96

  Alignments for each domain:
  == domain 1  score: 422.5 bits;  conditional E-value: 7.8e-131
                          TIGR00407   3 eaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvieL 78 
                                         a+ +la ls +  n++l+++ad+  ae+++il +n+kd+a   +   +++ +drL+Ltee+lk+ia+d ++v+ L
  lcl|FitnessBrowser__Btheta:353244  14 AASRELALLSDDTINQILNAVADATIAETSFILSENEKDLARMDK---SNPKYDRLKLTEERLKGIAADTRNVATL 86 
                                        68899***********************************97655...8999************************ PP

                          TIGR00407  79 adPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqda 154
                                        + P+G++++++++ +G+kl +v+vP Gv+g+iyearP+v  dv sLclk+Gna iLkGg++a  sn+a+++vi++ 
  lcl|FitnessBrowser__Btheta:353244  87 PSPLGRILKETSRPNGMKLTKVSVPFGVIGIIYEARPNVSFDVFSLCLKSGNACILKGGSDADDSNRAIISVIHKV 162
                                        **************************************************************************** PP

                          TIGR00407 155 leqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadlaka 230
                                        le+  +  + v+l+   dre    ll+   yvdl+iPrG+++l++ ++e+++iPv+e+++G+Ch+y de  d+ k 
  lcl|FitnessBrowser__Btheta:353244 163 LEKFHVNPHIVELLPA-DREATAALLNATGYVDLIIPRGSSNLINFVRENARIPVIETGAGICHTYFDEFGDTRKG 237
                                        **************98.*********************************************************** PP

                          TIGR00407 231 kkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlk.llelekateae.vskedfdke 304
                                          +i +akt+r s+Cna++  +++++     l++L +ql+e+ v++ ad+++ + l    +a+  + ++ e f +e
  lcl|FitnessBrowser__Btheta:353244 238 ADIIHNAKTRRVSVCNALDCTIIHEKRL-GDLPALCDQLKESKVTIYADTQAYQaLEGYYPAELLQpATPESFGTE 312
                                        ***********************99987.679****************877655155566676655245579**** PP

                          TIGR00407 305 flsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgist 380
                                        fl+ +++vk+v++ e+a+ hi++ +++hs++i+te+k+ a+ f+k vd+a vy n st f+dG +fG+Gae+gist
  lcl|FitnessBrowser__Btheta:353244 313 FLDYKMAVKTVKSFEDALGHIQENSSRHSECIVTENKERATLFTKIVDAACVYTNVSTAFTDGAQFGLGAEIGIST 388
                                        **************************************************************************** PP

                          TIGR00407 381 qklharGPvGLeaLvsyk 398
                                        qklharGP+GLe ++syk
  lcl|FitnessBrowser__Btheta:353244 389 QKLHARGPMGLEEITSYK 406
                                        *****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (417 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.87
//
[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