Alignments for a candidate for proA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Dinoroseobacter shibae DFL-12

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate 3608063 Dshi_1469 gamma-glutamyl phosphate reductase (RefSeq)

Query= BRENDA::A7Y114
         (420 letters)



>FitnessBrowser__Dino:3608063
          Length = 421

 Score =  342 bits (876), Expect = 2e-98
 Identities = 181/420 (43%), Positives = 255/420 (60%), Gaps = 5/420 (1%)

Query: 5   KDNVNVEAQAIE----AKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRN 60
           KD  ++ A   E    AK A+  L      ++  AL   AD +    + I+AAN +DL  
Sbjct: 2   KDFADIPALMAEIGTAAKAAAAELAFAPADQRAQALTAAADAVWARRDEIIAANARDLDY 61

Query: 61  GREQGFTEAFMDRLSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPL 120
           GR++G + A MDRL+L + RI+    GLR VA  +DP G  LS+W    GL + +V  PL
Sbjct: 62  GRDKGLSPAMMDRLALDEARIQGIVDGLRAVAAQDDPVGAVLSEWDRPTGLHIRRVRTPL 121

Query: 121 GVIGMIYEARPNVTVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQES 180
           GVIG+IYE+RPNVT DA  L LKSGNA++L+GGS + +S+  I   +   L    +P+ +
Sbjct: 122 GVIGVIYESRPNVTADAGALCLKSGNAVILRGGSESFHSSSLIHACLRDGLRAADLPETA 181

Query: 181 VQFIASTDRAATNQLFTMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKD 240
           +Q + + DRAA  ++ TM + +DV+IPRGG  L+  V   A VPV     G CHIY+D D
Sbjct: 182 IQLVPTRDRAAVGEMLTMTDTIDVIIPRGGKGLVGRVQAEARVPVFAHLEGICHIYVDAD 241

Query: 241 ADVEKAISILVNAKTDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLT 300
           AD +K   +++NAKT R  +C AAE L+V + W  ++    I+ L    + V  D+  L 
Sbjct: 242 ADPDKTARVILNAKTRRTGICGAAECLLVDRAWYDRNGATFIADLIAAGVEVRADD-TLQ 300

Query: 301 IIPDAVPAGEDDWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFL 360
            IP  VPA  DD+  E+L   IA + VD +  AIAHI  YG++H++ I+TEN   A +F 
Sbjct: 301 AIPGTVPAKADDFGREFLDMIIAARVVDGVDGAIAHIRRYGSQHTDCILTENDATAARFF 360

Query: 361 AIVDAAAIYHNASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420
             +D+A +  NAST+F DGG  G GAEIGI+T K+HARGP+G   LT+ K+L++G G IR
Sbjct: 361 QRLDSAILMRNASTQFADGGEFGMGAEIGIATGKMHARGPVGAEQLTSFKYLVEGDGTIR 420


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: 431
Number of extensions: 21
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: 420
Length of database: 421
Length adjustment: 32
Effective length of query: 388
Effective length of database: 389
Effective search space:   150932
Effective search space used:   150932
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 3608063 Dshi_1469 (gamma-glutamyl phosphate reductase (RefSeq))
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.27840.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.6e-137  443.0   0.0   5.4e-137  442.8   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608063  Dshi_1469 gamma-glutamyl phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608063  Dshi_1469 gamma-glutamyl phosphate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.8   0.0  5.4e-137  5.4e-137       1     398 []      18     410 ..      18     410 .. 0.99

  Alignments for each domain:
  == domain 1  score: 442.8 bits;  conditional E-value: 5.4e-137
                         TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvie 77 
                                       ak aa++la   ++++ +al++ ad++ a+ ++i+aana+d+  ++++Gl++a++drL+L+e+++++i+d+++ v+ 
  lcl|FitnessBrowser__Dino:3608063  18 AKAAAAELAFAPADQRAQALTAAADAVWARRDEIIAANARDLDYGRDKGLSPAMMDRLALDEARIQGIVDGLRAVAA 94 
                                       899************************************************************************** PP

                         TIGR00407  78 LadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqda 154
                                        +dPvG v+++ ++  GL+++rvr+PlGv+gviye+rP+v++d+ +Lclk+GnaviL+Gg+e+ +s   + + ++d 
  lcl|FitnessBrowser__Dino:3608063  95 QDDPVGAVLSEWDRPTGLHIRRVRTPLGVIGVIYESRPNVTADAGALCLKSGNAVILRGGSESFHSSSLIHACLRDG 171
                                       ***************************************************************************** PP

                         TIGR00407 155 leqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadlakak 231
                                       l+ + lp +a+ql+ + dr+ v e+l++ + +d++iPrGg++lv  ++ e+++Pv+ h +G+Chiy+d++ad  k  
  lcl|FitnessBrowser__Dino:3608063 172 LRAADLPETAIQLVPTRDRAAVGEMLTMTDTIDVIIPRGGKGLVGRVQAEARVPVFAHLEGICHIYVDADADPDKTA 248
                                       ***************************************************************************** PP

                         TIGR00407 232 kvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdkeflsl 308
                                       +vi++akt+r   C a e LLv++a+ ++   ++   l ++gve+rad++ +++  + +a+      +df +efl++
  lcl|FitnessBrowser__Dino:3608063 249 RVILNAKTRRTGICGAAECLLVDRAWYDRNGATFIADLIAAGVEVRADDTLQAIPGTVPAKA-----DDFGREFLDM 320
                                       **************************************************999987776554.....89******** PP

                         TIGR00407 309 dLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklha 385
                                       ++++++v+ ++ ai+hir+yg++h+d+ilte++++a +f ++ dsa    nast+fadG++fG+Gae+gi+t k+ha
  lcl|FitnessBrowser__Dino:3608063 321 IIAARVVDGVDGAIAHIRRYGSQHTDCILTENDATAARFFQRLDSAILMRNASTQFADGGEFGMGAEIGIATGKMHA 397
                                       ***************************************************************************** PP

                         TIGR00407 386 rGPvGLeaLvsyk 398
                                       rGPvG e L+s+k
  lcl|FitnessBrowser__Dino:3608063 398 RGPVGAEQLTSFK 410
                                       ***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 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: 00:00:00.02
# Mc/sec: 7.14
//
[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