Alignments for a candidate for proA in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Paraburkholderia bryophila 376MFSha3.1

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate H281DRAFT_06324 H281DRAFT_06324 glutamate-5-semialdehyde dehydrogenase

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__Burk376:H281DRAFT_06324
          Length = 423

 Score =  368 bits (945), Expect = e-106
 Identities = 191/411 (46%), Positives = 272/411 (66%), Gaps = 1/411 (0%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           +  +G  A+QAS  +A+ S+  KN  L  +A  +E  + ++  ANA+D+A AR  G   A
Sbjct: 7   MTDLGRRARQASRAMARASTAAKNAALAAVAAGIERDAALLKEANARDLARARDKGHDAA 66

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
            +DRL L+   LK + + +RQV  LADP+G++ +     SG+++ + RVPLGVIG+IYE+
Sbjct: 67  FIDRLTLSDKALKTMVEGLRQVAALADPIGEISNLKYRPSGIQVGQMRVPLGVIGIIYES 126

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVT+D A+LCLK+GNA ILRGG E    N A   +I + L++ GLP  AVQ +   DR
Sbjct: 127 RPNVTIDAAALCLKSGNATILRGGSEALECNTALAKLIGEGLEAAGLPQDAVQVVATADR 186

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
           A V +++ M +Y+D+++PRGG  L +    ++ +P+I    G+CH+YVD+  ++A+AL V
Sbjct: 187 AAVGKLITMTEYVDVIVPRGGKSLIERLMNEARVPMIKHLDGICHVYVDDRADLAKALTV 246

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQ-AGPAK 300
             NAKT R  TCNT+ETLLV + IA + LP L K   E  V L  DAAA A L  AG   
Sbjct: 247 CDNAKTHRYGTCNTMETLLVARGIASTVLPPLGKLYREKEVELRVDAAARAVLAGAGVGP 306

Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360
           +V    +++  E+L+  L +K+V DLD AI HI  + +QH+DAI+T D   A RF+ EVD
Sbjct: 307 LVDATEDDWRTEYLAPVLAIKVVDDLDAAIEHINTYSSQHTDAIVTEDHDRAMRFLREVD 366

Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIG 411
           S++V VNASTRF DG +FGLGAE+ +S  KLHARGP+GLE LT+ K++ +G
Sbjct: 367 SASVMVNASTRFADGFEFGLGAEIGISNDKLHARGPVGLEGLTSLKYVVLG 417


Lambda     K      H
   0.317    0.133    0.369 

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: 429
Number of extensions: 18
Number of successful extensions: 2
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: 417
Length of database: 423
Length adjustment: 32
Effective length of query: 385
Effective length of database: 391
Effective search space:   150535
Effective search space used:   150535
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate H281DRAFT_06324 H281DRAFT_06324 (glutamate-5-semialdehyde dehydrogenase)
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.30973.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.1e-152  494.5   1.9   1.2e-152  494.3   1.9    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_06324  H281DRAFT_06324 glutamate-5-semi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06324  H281DRAFT_06324 glutamate-5-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.3   1.9  1.2e-152  1.2e-152       1     398 []      14     412 ..      14     412 .. 0.98

  Alignments for each domain:
  == domain 1  score: 494.3 bits;  conditional E-value: 1.2e-152
                                    TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklk 66 
                                                  a++a+  +a  sta kn al+++a +++++a l+ +ana+d+a a+++G   a++drL+L+++ lk
  lcl|FitnessBrowser__Burk376:H281DRAFT_06324  14 ARQASRAMARASTAAKNAALAAVAAGIERDAALLKEANARDLARARDKGHDAAFIDRLTLSDKALK 79 
                                                  89**************************************************************** PP

                                    TIGR00407  67 siaddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnav 132
                                                  ++++++++v+ LadP+G++ + + + +G+++ ++rvPlGv+g+iye+rP+v++d+a+Lclk+Gna 
  lcl|FitnessBrowser__Burk376:H281DRAFT_06324  80 TMVEGLRQVAALADPIGEISNLKYRPSGIQVGQMRVPLGVIGIIYESRPNVTIDAAALCLKSGNAT 145
                                                  ****************************************************************** PP

                                    TIGR00407 133 iLkGgkeavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelv 198
                                                  iL+Gg+ea + n al+++i + le +glp+ avq++ ++dr+ v +l+++ eyvd+++PrGg++l+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06324 146 ILRGGSEALECNTALAKLIGEGLEAAGLPQDAVQVVATADRAAVGKLITMTEYVDVIVPRGGKSLI 211
                                                  ****************************************************************** PP

                                    TIGR00407 199 klikeestiPvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeeflee 264
                                                  + + +e+++P+++h dG+Ch+y+d+ adlaka +v ++akt+r  tCn++etLLv + ia+  l+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_06324 212 ERLMNEARVPMIKHLDGICHVYVDDRADLAKALTVCDNAKTHRYGTCNTMETLLVARGIASTVLPP 277
                                                  ****************************************************************** PP

                                    TIGR00407 265 Lekqleekgvelradalvlklleleka.teaevskedfdkeflsldLsvkivedleeaiehirqyg 329
                                                  L k   ek+velr da++ ++l  +++   ++++++d+++e+l+++L++k+v+dl++aiehi++y+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06324 278 LGKLYREKEVELRVDAAARAVLAGAGVgPLVDATEDDWRTEYLAPVLAIKVVDDLDAAIEHINTYS 343
                                                  *****************999887666515789999******************************* PP

                                    TIGR00407 330 tkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLv 395
                                                  ++h+dai+ted+  a +f++evdsa+v vnastrfadGf+fG+Gae+gis +klharGPvGLe+L+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06324 344 SQHTDAIVTEDHDRAMRFLREVDSASVMVNASTRFADGFEFGLGAEIGISNDKLHARGPVGLEGLT 409
                                                  ****************************************************************** PP

                                    TIGR00407 396 syk 398
                                                  s k
  lcl|FitnessBrowser__Burk376:H281DRAFT_06324 410 SLK 412
                                                  976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (423 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.50
//
[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