Alignments for a candidate for proA in Persephonella marina EX-H1

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Persephonella marina EX-H1

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_012676561.1 PERMA_RS08340 gamma-glutamyl-phosphate reductase

Query= BRENDA::A7Y114
         (420 letters)



>NCBI__GCF_000021565.1:WP_012676561.1
          Length = 445

 Score =  384 bits (985), Expect = e-111
 Identities = 201/418 (48%), Positives = 279/418 (66%), Gaps = 8/418 (1%)

Query: 11  EAQAIEAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEAF 70
           E  A EA+++ K L  ++   KN  L   A++L    E I  AN+KDL   +++G+++A 
Sbjct: 8   EKLAREARESQKFLRRVTTDIKNRVLLRTAELLIEKKEIIKEANDKDLEFAQKKGYSKAL 67

Query: 71  MDRLSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEAR 130
           +DRL+L+++RI    Q L+DVA L DP G+ +S WT  NGL+V ++ VPLG + +IYEAR
Sbjct: 68  LDRLTLNEKRINGMVQVLKDVASLPDPVGEIISMWTRPNGLRVGQMRVPLGTVMIIYEAR 127

Query: 131 PNVTVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDRA 190
           PNVTV+A  L +KS NA++LKGGS  INSN+ +VE++ +A  E+  P+ ++QF+ +TDR 
Sbjct: 128 PNVTVEAASLCIKSSNAVILKGGSETINSNRVLVEILRQAARESGFPERAIQFVDTTDRE 187

Query: 191 ATNQLFTMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISIL 250
           A N L T+ +++DV+IPRGG  LI+AV E AT+PV++   G C++YID +AD+EKA++I 
Sbjct: 188 AVNHLLTLDQYIDVVIPRGGEGLIRAVAEKATMPVIKHYKGVCNLYIDDEADMEKALNIA 247

Query: 251 VNAKTDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPD------ 304
            NAK +RP+VCNA E LIVHKD   +   E+     K  + +  DE  L I+ D      
Sbjct: 248 YNAKVERPSVCNAIENLIVHKDIAEKFLPEIAYYYGKAGVEMRCDERALEILRDHPKAND 307

Query: 305 --AVPAGEDDWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAI 362
              VPA EDD+  E+L   IAVK VD +  AI  I  YG+ HSE+IVTEN     +F+  
Sbjct: 308 TEIVPAKEDDYYEEFLDLIIAVKVVDSIDQAIDFIHKYGSNHSESIVTENYTKGMRFINE 367

Query: 363 VDAAAIYHNASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420
           VD++A+Y NASTRFTDG   G GAE+GIST K+H RGPMGL  LT  KF++ G GQIR
Sbjct: 368 VDSSAVYINASTRFTDGNEFGLGAEMGISTDKIHVRGPMGLKELTIPKFIIFGDGQIR 425


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: 468
Number of extensions: 22
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: 445
Length adjustment: 32
Effective length of query: 388
Effective length of database: 413
Effective search space:   160244
Effective search space used:   160244
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: 51 (24.3 bits)

Align candidate WP_012676561.1 PERMA_RS08340 (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.7248.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-153  496.0   0.7   4.5e-153  495.7   0.7    1.0  1  lcl|NCBI__GCF_000021565.1:WP_012676561.1  PERMA_RS08340 gamma-glutamyl-pho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021565.1:WP_012676561.1  PERMA_RS08340 gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.7   0.7  4.5e-153  4.5e-153       1     395 [.      14     412 ..      14     415 .. 0.96

  Alignments for each domain:
  == domain 1  score: 495.7 bits;  conditional E-value: 4.5e-153
                                 TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 
                                               a+e+   l  ++t+ kn++l   a+ L ++ e+i +an kd++ a+++G ++alldrL+L+e+++++++
  lcl|NCBI__GCF_000021565.1:WP_012676561.1  14 ARESQKFLRRVTTDIKNRVLLRTAELLIEKKEIIKEANDKDLEFAQKKGYSKALLDRLTLNEKRINGMV 82 
                                               78888999************************************************************* PP

                                 TIGR00407  70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138
                                               + +kdv++L+dPvG++i+  ++ +GL++ ++rvPlG + +iyearP+v+v++asLc+k+ naviLkGg+
  lcl|NCBI__GCF_000021565.1:WP_012676561.1  83 QVLKDVASLPDPVGEIISMWTRPNGLRVGQMRVPLGTVMIIYEARPNVTVEAASLCIKSSNAVILKGGS 151
                                               ********************************************************************* PP

                                 TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207
                                               e+++sn++lve++++a +++g p  a+q ++++dre v++ll+ld+y+d++iPrGg++l++ + e++t+
  lcl|NCBI__GCF_000021565.1:WP_012676561.1 152 ETINSNRVLVEILRQAARESGFPERAIQFVDTTDREAVNHLLTLDQYIDVVIPRGGEGLIRAVAEKATM 220
                                               ********************************************************************* PP

                                 TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276
                                               Pv++h +GvC++y+d++ad++ka ++  +ak +rPs+Cnaie L+v+k+iae+fl+e++    ++gve+
  lcl|NCBI__GCF_000021565.1:WP_012676561.1 221 PVIKHYKGVCNLYIDDEADMEKALNIAYNAKVERPSVCNAIENLIVHKDIAEKFLPEIAYYYGKAGVEM 289
                                               ********************************************************************* PP

                                 TIGR00407 277 radalvlkllele.kate...aevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedk 341
                                               r d+ +l++l+   ka++   + ++++d+ +efl+l+++vk+v+++++ai+ i++yg++hs++i+te+ 
  lcl|NCBI__GCF_000021565.1:WP_012676561.1 290 RCDERALEILRDHpKANDteiVPAKEDDYYEEFLDLIIAVKVVDSIDQAIDFIHKYGSNHSESIVTENY 358
                                               ****99998754314444111446677****************************************** PP

                                 TIGR00407 342 knaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLv 395
                                               ++  +f++evds+avy nastrf+dG +fG+Gae+gist+k+h rGP+GL+ L+
  lcl|NCBI__GCF_000021565.1:WP_012676561.1 359 TKGMRFINEVDSSAVYINASTRFTDGNEFGLGAEMGISTDKIHVRGPMGLKELT 412
                                               ***************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (445 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: 10.94
//
[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