Alignments for a candidate for proA in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Caulobacter crescentus NA1000

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate CCNA_03543 CCNA_03543 gamma-glutamyl phosphate reductase

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__Caulo:CCNA_03543
          Length = 424

 Score =  323 bits (828), Expect = 6e-93
 Identities = 172/405 (42%), Positives = 256/405 (63%), Gaps = 5/405 (1%)

Query: 5   MGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEAMLD 64
           MG  A++ +  L   +  ++   ++ +A  +   ++ IL ANA+D+A A ANG+S  MLD
Sbjct: 15  MGRTAREGARALRLATPEQRTAAIQAMAVAIREDADAILTANAKDLARAEANGVSGPMLD 74

Query: 65  RLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEARPN 124
           RLAL  ARL+G+A  V  V  + DPVG         +GL + R R P+GVI +IYE+RPN
Sbjct: 75  RLALDAARLEGVAAGVEAVAAVPDPVGVATSRWTRPNGLDIARVRTPIGVIAMIYESRPN 134

Query: 125 VTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDRALV 184
           VT D A+LC+++GNAVILRGG E   +N A  A I   L+  GLP  AVQA+  PDRA V
Sbjct: 135 VTADAAALCVRSGNAVILRGGSECIHSNLAIHAAIARGLQKAGLPTAAVQAVKTPDRAAV 194

Query: 185 SEMLR-MDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKVIV 243
             +L  +D+ ID++IPRGG  L    + ++  PV+    G+ H++V  + ++ +A++V+V
Sbjct: 195 GMILAGLDRTIDLIIPRGGKSLVARVQAEARAPVLGHLEGLNHVFVHAAADLKKAVEVVV 254

Query: 244 NAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKVVA 303
           NAK +R S C + ETLL+++  AD  LP ++  + ++G  L  DAAA    +A    +  
Sbjct: 255 NAKLRRVSVCGSAETLLIDQAAADKLLPPIADALIKAGCELRGDAAA----RAIEPTMKK 310

Query: 304 VKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDSSA 363
              E++  E+L+  L+V +V  +  A  HI  +G+ H+DAI+T D   A+ F+ EVDS+ 
Sbjct: 311 ATVEDWTTEYLAPILSVAVVDGVAGAARHIASYGSGHTDAIITEDAAAAEAFIAEVDSAI 370

Query: 364 VYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWI 408
           V VNAST+F DGG+FG GAE+ ++T KLHARGP+G E LTT+K++
Sbjct: 371 VLVNASTQFADGGEFGFGAEIGIATDKLHARGPVGAEQLTTFKYV 415


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: 424
Number of extensions: 19
Number of successful extensions: 3
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: 424
Length adjustment: 32
Effective length of query: 385
Effective length of database: 392
Effective search space:   150920
Effective search space used:   150920
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 CCNA_03543 CCNA_03543 (gamma-glutamyl phosphate reductase)
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.19383.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-136  441.2   3.3   1.9e-136  441.0   3.3    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03543  CCNA_03543 gamma-glutamyl phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03543  CCNA_03543 gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.0   3.3  1.9e-136  1.9e-136       1     398 []      19     413 ..      19     413 .. 0.98

  Alignments for each domain:
  == domain 1  score: 441.0 bits;  conditional E-value: 1.9e-136
                             TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvk 73 
                                           a+e a  l   + +++  a++++a +++++a++il anakd+a a++nG++ ++ldrL+L+ ++l+++a++v+
  lcl|FitnessBrowser__Caulo:CCNA_03543  19 AREGARALRLATPEQRTAAIQAMAVAIREDADAILTANAKDLARAEANGVSGPMLDRLALDAARLEGVAAGVE 91 
                                           7899999999*************************************************************** PP

                             TIGR00407  74 dvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnka 146
                                            v+ ++dPvG  ++  ++ +GL + rvr+P+Gv+ +iye+rP+v++d+a+Lc+++GnaviL+Gg+e+++sn a
  lcl|FitnessBrowser__Caulo:CCNA_03543  92 AVAAVPDPVGVATSRWTRPNGLDIARVRTPIGVIAMIYESRPNVTADAAALCVRSGNAVILRGGSECIHSNLA 164
                                           ************************************************************************* PP

                             TIGR00407 147 lveviqdaleqtglpveavqliedpdreevkell.kldeyvdlliPrGgnelvklikeestiPvlehadGvCh 218
                                           + + i + l+++glp+ avq++++pdr+ v  +l  ld+ +dl+iPrGg++lv  ++ e++ Pvl+h +G  h
  lcl|FitnessBrowser__Caulo:CCNA_03543 165 IHAAIARGLQKAGLPTAAVQAVKTPDRAAVGMILaGLDRTIDLIIPRGGKSLVARVQAEARAPVLGHLEGLNH 237
                                           ******************************887736************************************* PP

                             TIGR00407 219 iyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlklleleka 291
                                           +++ + adl+ka +v+v+ak +r s+C + etLL+++a a++ l+ ++++l ++g elr+da++ ++ ++   
  lcl|FitnessBrowser__Caulo:CCNA_03543 238 VFVHAAADLKKAVEVVVNAKLRRVSVCGSAETLLIDQAAADKLLPPIADALIKAGCELRGDAAARAIEPTM-- 308
                                           *****************************************************************999877.. PP

                             TIGR00407 292 teaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrf 364
                                           ++  ++ ed+ +e+l+++Lsv +v+ +  a +hi  yg+ h+dai+ted ++ae f+ evdsa v vnast+f
  lcl|FitnessBrowser__Caulo:CCNA_03543 309 KK--ATVEDWTTEYLAPILSVAVVDGVAGAARHIASYGSGHTDAIITEDAAAAEAFIAEVDSAIVLVNASTQF 379
                                           34..44579**************************************************************** PP

                             TIGR00407 365 adGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                           adG++fGfGae+gi+t+klharGPvG e L+++k
  lcl|FitnessBrowser__Caulo:CCNA_03543 380 ADGGEFGFGAEIGIATDKLHARGPVGAEQLTTFK 413
                                           *******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (424 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: 8.58
//
[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