Alignments for a candidate for proA in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Phaeobacter inhibens BS107

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate GFF1533 PGA1_c15520 gamma-glutamyl phosphate reductase ProA

Query= BRENDA::A7Y114
         (420 letters)



>FitnessBrowser__Phaeo:GFF1533
          Length = 421

 Score =  345 bits (885), Expect = 1e-99
 Identities = 181/405 (44%), Positives = 258/405 (63%), Gaps = 3/405 (0%)

Query: 17  AKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEAFMDRLSL 76
           AK+A+  L   + + K DAL+  AD +      IL AN KDL  GR +G + A MDRL+L
Sbjct: 18  AKQAAAKLATATAERKADALNAAADAVWDARAEILGANAKDLDFGRNKGLSPAMMDRLAL 77

Query: 77  SQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEARPNVTVD 136
            ++RI     GLR VA   DP G+ L++W+  +GL +++V  PLGVIG+IYE+RPNVT D
Sbjct: 78  DEDRISGIVAGLRAVAAQPDPVGEVLAEWSQPSGLDIQRVRTPLGVIGVIYESRPNVTAD 137

Query: 137 ATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDRAATNQLF 196
           A  L LKSGNA++L+GGS +  S+QAI   +   L    +P++++Q + + DRAA  +L 
Sbjct: 138 AGALCLKSGNAVILRGGSESFYSSQAIHGCLAAGLRAADLPEDAIQLVPTRDRAAVQELL 197

Query: 197 TMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISILVNAKTD 256
           TM + VDV++PRGG  L+  V   A VPV     G  HIY+DKDAD +KA+ I++NAKT 
Sbjct: 198 TMTDTVDVIVPRGGKGLVGLVQREARVPVFAHLEGIVHIYLDKDADPQKALEIVLNAKTR 257

Query: 257 RPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAVPAGED-DWKN 315
           R  +C AAE L++H+D       ++++AL    + +  +  +    PD + A    DW  
Sbjct: 258 RTGICGAAECLLIHRDIAETIGRDVLTALATAGVEIRAEAGLPG--PDGMTAATSADWGC 315

Query: 316 EYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAIYHNASTR 375
           EYL   IA K VDD+  AI HI T+ ++H++ I+TEN  A  +F A +D+A + HNAST+
Sbjct: 316 EYLDAIIAAKQVDDIDAAIDHIRTHHSQHTDCIITENDSAVAQFFAELDSAILMHNASTQ 375

Query: 376 FTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420
           F DGG  G GAEIGI+T K+HARGP+G   LT+ K+L++G G +R
Sbjct: 376 FADGGEFGMGAEIGIATGKMHARGPVGAAQLTSFKYLVRGHGALR 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: 440
Number of extensions: 17
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 GFF1533 PGA1_c15520 (gamma-glutamyl phosphate reductase ProA)
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.13728.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   5.3e-137  442.8   0.2   6.1e-137  442.6   0.2    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1533  PGA1_c15520 gamma-glutamyl phosp


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1533  PGA1_c15520 gamma-glutamyl phosphate reductase ProA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.6   0.2  6.1e-137  6.1e-137       1     398 []      18     410 ..      18     410 .. 0.98

  Alignments for each domain:
  == domain 1  score: 442.6 bits;  conditional E-value: 6.1e-137
                          TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvi 76 
                                        ak+aa+kla+ +++ k +al++ ad++  +  +il anakd+  ++++Gl++a++drL+L+e+++ +i+++++ v+
  lcl|FitnessBrowser__Phaeo:GFF1533  18 AKQAAAKLATATAERKADALNAAADAVWDARAEILGANAKDLDFGRNKGLSPAMMDRLALDEDRISGIVAGLRAVA 93 
                                        8*************************************************************************** PP

                          TIGR00407  77 eLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviq 152
                                          +dPvG+v+ + +  +GL ++rvr+PlGv+gviye+rP+v++d+ +Lclk+GnaviL+Gg+e+  s +a+   + 
  lcl|FitnessBrowser__Phaeo:GFF1533  94 AQPDPVGEVLAEWSQPSGLDIQRVRTPLGVIGVIYESRPNVTADAGALCLKSGNAVILRGGSESFYSSQAIHGCLA 169
                                        **************************************************************************** PP

                          TIGR00407 153 daleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadla 228
                                          l+ + lp  a+ql+ + dr+ v+ell++ + vd+++PrGg++lv l+++e+++Pv+ h +G+ hiyld++ad +
  lcl|FitnessBrowser__Phaeo:GFF1533 170 AGLRAADLPEDAIQLVPTRDRAAVQELLTMTDTVDVIVPRGGKGLVGLVQREARVPVFAHLEGIVHIYLDKDADPQ 245
                                        **************************************************************************** PP

                          TIGR00407 229 kakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdke 304
                                        ka +++++akt+r   C a e LL++++iae   + +  +l+ +gve+ra+a       ++      ++  d+  e
  lcl|FitnessBrowser__Phaeo:GFF1533 246 KALEIVLNAKTRRTGICGAAECLLIHRDIAETIGRDVLTALATAGVEIRAEAGLPGPDGMTA-----ATSADWGCE 316
                                        ***************************************************99876555553.....34468999* PP

                          TIGR00407 305 flsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgist 380
                                        +l+ ++++k v+d+++ai+hir++ ++h+d+i+te++++  +f  e dsa   +nast+fadG++fG+Gae+gi+t
  lcl|FitnessBrowser__Phaeo:GFF1533 317 YLDAIIAAKQVDDIDAAIDHIRTHHSQHTDCIITENDSAVAQFFAELDSAILMHNASTQFADGGEFGMGAEIGIAT 392
                                        **************************************************************************** PP

                          TIGR00407 381 qklharGPvGLeaLvsyk 398
                                         k+harGPvG   L+s+k
  lcl|FitnessBrowser__Phaeo:GFF1533 393 GKMHARGPVGAAQLTSFK 410
                                        ***************987 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: 00:00:00.01
# Mc/sec: 9.59
//
[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