Alignments for a candidate for proA in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Chlorobium phaeobacteroides BS1

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_012474300.1 CPHAMN1_RS04305 gamma-glutamyl-phosphate reductase

Query= BRENDA::A7Y114
         (420 letters)



>NCBI__GCF_000020545.1:WP_012474300.1
          Length = 417

 Score =  314 bits (805), Expect = 3e-90
 Identities = 178/417 (42%), Positives = 252/417 (60%), Gaps = 17/417 (4%)

Query: 13  QAIEAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEAFMD 72
           Q  + ++AS+ L  LSD + N  L+ +A+ +  + + IL AN+KDL         +   D
Sbjct: 8   QLEKVREASRKLCTLSDSDINSLLNDLANRIPGNSQTILEANQKDLDR---MDPNDPKYD 64

Query: 73  RLSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEARPN 132
           RL LS  R+   A  +R+VAEL  P G+ L   TL NGL ++K TVPLGV+G+IYE+RPN
Sbjct: 65  RLLLSTSRLESIASDIRNVAELPTPVGRILEKRTLPNGLALKKTTVPLGVVGIIYESRPN 124

Query: 133 VTVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDRAAT 192
           VT D   L LKSGNA VLKGGS A+ SN AIV++I + L    +  +++  + S DR A 
Sbjct: 125 VTFDVFALCLKSGNATVLKGGSDAMYSNMAIVDLIREVLVRNNVNPDTLYLLPS-DREAA 183

Query: 193 NQLFTMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISILVN 252
             +     ++DV+IPRG  +LI    ++++VPV+ETG G  H Y D   D++    I+ N
Sbjct: 184 GIMLNAVGYIDVIIPRGSQQLIDFARKSSSVPVIETGAGIVHTYFDLSGDLQMGKEIVFN 243

Query: 253 AKTDRPAVCNAAETLIVHKDWLAQHSDELISA---LKKENIHVHGDEHVLTIIPDAVP-- 307
           AKT RP+VCNA +TL++H++ L    D+L S    L ++ + +  D+     +    P  
Sbjct: 244 AKTRRPSVCNALDTLLIHRERL----DDLASIAEPLAEKKVIIFADKDAYPALLSRYPSE 299

Query: 308 ----AGEDDWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIV 363
               A E  +  E+LS  ++VK VD L DA+ HI  + + HSEA++  +    D+FL  V
Sbjct: 300 LLQKAEEKHFGTEFLSLKMSVKTVDSLEDALKHIARFSSMHSEAVIASDAVVKDEFLKRV 359

Query: 364 DAAAIYHNASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420
           DAA +Y N ST FTDG   G GAEIGISTQKLHARGPM L  LT+ K++++G GQ R
Sbjct: 360 DAAVVYANTSTAFTDGAQFGLGAEIGISTQKLHARGPMALQELTSYKWVIEGDGQTR 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: 422
Number of extensions: 22
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 WP_012474300.1 CPHAMN1_RS04305 (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.9710.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-127  411.8   0.0   1.6e-127  411.6   0.0    1.0  1  lcl|NCBI__GCF_000020545.1:WP_012474300.1  CPHAMN1_RS04305 gamma-glutamyl-p


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020545.1:WP_012474300.1  CPHAMN1_RS04305 gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.6   0.0  1.6e-127  1.6e-127       2     398 .]      13     406 ..      12     406 .. 0.95

  Alignments for each domain:
  == domain 1  score: 411.6 bits;  conditional E-value: 1.6e-127
                                 TIGR00407   2 keaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiad 70 
                                               +ea+ kl +ls  + n++l+ +a+ +  ++++il+an+kd+         d+ +drLlL+ ++l+sia 
  lcl|NCBI__GCF_000020545.1:WP_012474300.1  13 REASRKLCTLSDSDINSLLNDLANRIPGNSQTILEANQKDLDRMDP---NDPKYDRLLLSTSRLESIAS 78 
                                               89***************************************87666...5999**************** PP

                                 TIGR00407  71 dvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgke 139
                                               d+++v+eL+ PvG+++e+r+l +GL l++ +vPlGv+g+iye+rP+v+ dv +Lclk+Gna +LkGg++
  lcl|NCBI__GCF_000020545.1:WP_012474300.1  79 DIRNVAELPTPVGRILEKRTLPNGLALKKTTVPLGVVGIIYESRPNVTFDVFALCLKSGNATVLKGGSD 147
                                               ********************************************************************* PP

                                 TIGR00407 140 avrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiP 208
                                               a+ sn a+v++i++ l +  +   ++ l+   dre +  +l+   y+d++iPrG+++l++  +++s +P
  lcl|NCBI__GCF_000020545.1:WP_012474300.1 148 AMYSNMAIVDLIREVLVRNNVNPDTLYLLPS-DREAAGIMLNAVGYIDVIIPRGSQQLIDFARKSSSVP 215
                                               *****************************99.************************************* PP

                                 TIGR00407 209 vlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelr 277
                                               v+e+++G+ h+y d s dl++ k+++ +akt+rPs+Cna++tLL++++  +  l ++++ l+ek v + 
  lcl|NCBI__GCF_000020545.1:WP_012474300.1 216 VIETGAGIVHTYFDLSGDLQMGKEIVFNAKTRRPSVCNALDTLLIHRERLD-DLASIAEPLAEKKVIIF 283
                                               ***********************************************9995.578999*********** PP

                                 TIGR00407 278 adalv.lkllelekateaev.skedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkkna 344
                                               ad+ +  +ll+  + +  ++  +++f +eflsl++svk+v++le+a++hi ++++ hs+a++++d    
  lcl|NCBI__GCF_000020545.1:WP_012474300.1 284 ADKDAyPALLSRYPSELLQKaEEKHFGTEFLSLKMSVKTVDSLEDALKHIARFSSMHSEAVIASDAVVK 352
                                               9765514556555555544404558******************************************** PP

                                 TIGR00407 345 ekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                               ++f+k+vd+a vy n+st f+dG +fG+Gae+gistqklharGP+ L+ L+syk
  lcl|NCBI__GCF_000020545.1:WP_012474300.1 353 DEFLKRVDAAVVYANTSTAFTDGAQFGLGAEIGISTQKLHARGPMALQELTSYK 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.39
//
[ok]

This GapMind analysis is from Apr 10 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