Alignments for a candidate for proA in Desulfatiglans anilini DSM 4660

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Desulfatiglans anilini DSM 4660

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_028320041.1 H567_RS0101530 glutamate-5-semialdehyde dehydrogenase

Query= BRENDA::A7Y114
         (420 letters)



>NCBI__GCF_000422285.1:WP_028320041.1
          Length = 418

 Score =  371 bits (953), Expect = e-107
 Identities = 190/411 (46%), Positives = 265/411 (64%)

Query: 10  VEAQAIEAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEA 69
           +   A EA +A+++L  +   +K+ AL+ +A +L R  + I   N +D+   RE G + A
Sbjct: 7   IRTMADEAGRAARALRSIGRADKDAALNRMAGLLRRYSDRISEENAQDVARAREAGLSAA 66

Query: 70  FMDRLSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEA 129
            +DRL+L+   I   AQGL +VA L DP G     W   NGL V +V +P+GVIG IYE+
Sbjct: 67  MIDRLTLTGPTIEGMAQGLEEVAGLPDPVGMVTGMWRRPNGLLVGRVRIPIGVIGFIYES 126

Query: 130 RPNVTVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDR 189
           RPNVTVDA  L LKSGNA++LKGGS AI SN  + E++ +AL ET +P+++VQ + +TDR
Sbjct: 127 RPNVTVDAAALCLKSGNAVILKGGSEAIQSNMVLAEILAEALRETGLPEKAVQVVPTTDR 186

Query: 190 AATNQLFTMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISI 249
            A + L  + E VD++IPRGG  LI+ V +++ +PVL+   G CH+Y+D+DA++  A  I
Sbjct: 187 EAVSILIGLDEDVDLIIPRGGEGLIRFVADHSKIPVLKHYKGVCHVYVDQDAEIPMAEEI 246

Query: 250 LVNAKTDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAVPAG 309
             NAK  RP VCNA ETL+VH+    +    +I   +K  + + G E   +I P    A 
Sbjct: 247 CYNAKVQRPGVCNAMETLLVHEGIAGRFLPAMIERFEKAGVEIRGCERTRSIAPQVRAAV 306

Query: 310 EDDWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAIY 369
            +DW  E+L   +AVK V DL +A+ HIE YG+KH+E IVT +   A +FL  VD++ + 
Sbjct: 307 AEDWPAEFLDLILAVKVVGDLEEALDHIERYGSKHTETIVTNDYARAQRFLGEVDSSVVL 366

Query: 370 HNASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420
            NASTRF DG  LG GAEIGI+T KLHA GPMGL  LTT KF++ G+GQ+R
Sbjct: 367 VNASTRFNDGNQLGLGAEIGINTSKLHAFGPMGLEELTTTKFIVYGSGQVR 417


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: 26
Number of successful extensions: 1
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: 418
Length adjustment: 32
Effective length of query: 388
Effective length of database: 386
Effective search space:   149768
Effective search space used:   149768
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_028320041.1 H567_RS0101530 (glutamate-5-semialdehyde dehydrogenase)
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.1786.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.9e-152  491.6   0.0   9.1e-152  491.4   0.0    1.0  1  lcl|NCBI__GCF_000422285.1:WP_028320041.1  H567_RS0101530 glutamate-5-semia


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000422285.1:WP_028320041.1  H567_RS0101530 glutamate-5-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  491.4   0.0  9.1e-152  9.1e-152       3     398 .]      16     407 ..      14     407 .. 0.98

  Alignments for each domain:
  == domain 1  score: 491.4 bits;  conditional E-value: 9.1e-152
                                 TIGR00407   3 eaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiadd 71 
                                               +aa  l ++  a+k+ al+ +a  L++ ++ i ++na+d+a a+e Gl+ a++drL+Lt   ++++a++
  lcl|NCBI__GCF_000422285.1:WP_028320041.1  16 RAARALRSIGRADKDAALNRMAGLLRRYSDRISEENAQDVARAREAGLSAAMIDRLTLTGPTIEGMAQG 84 
                                               7999***************************************************************** PP

                                 TIGR00407  72 vkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkea 140
                                               +++v+ L+dPvG v+   ++ +GL + rvr+P+Gv+g iye+rP+v+vd+a+Lclk+GnaviLkGg+ea
  lcl|NCBI__GCF_000422285.1:WP_028320041.1  85 LEEVAGLPDPVGMVTGMWRRPNGLLVGRVRIPIGVIGFIYESRPNVTVDAAALCLKSGNAVILKGGSEA 153
                                               ********************************************************************* PP

                                 TIGR00407 141 vrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPv 209
                                               ++sn +l+e++ +al++tglp +avq++ ++dre v+ l+ lde vdl+iPrGg++l++ + ++s+iPv
  lcl|NCBI__GCF_000422285.1:WP_028320041.1 154 IQSNMVLAEILAEALRETGLPEKAVQVVPTTDREAVSILIGLDEDVDLIIPRGGEGLIRFVADHSKIPV 222
                                               ********************************************************************* PP

                                 TIGR00407 210 lehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelra 278
                                               l+h +GvCh+y+d++a++ +a+++  +ak qrP +Cna+etLLv++ ia +fl+++ ++ e++gve+r+
  lcl|NCBI__GCF_000422285.1:WP_028320041.1 223 LKHYKGVCHVYVDQDAEIPMAEEICYNAKVQRPGVCNAMETLLVHEGIAGRFLPAMIERFEKAGVEIRG 291
                                               ********************************************************************* PP

                                 TIGR00407 279 dalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekf 347
                                                + +  + ++ +a +    +ed+  efl+l+L+vk+v dleea++hi++yg+kh+++i+t+d + a++f
  lcl|NCBI__GCF_000422285.1:WP_028320041.1 292 CERTRSIAPQVRAAV----AEDWPAEFLDLILAVKVVGDLEEALDHIERYGSKHTETIVTNDYARAQRF 356
                                               ****99999885554....589*********************************************** PP

                                 TIGR00407 348 vkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                               + evds+ v vnastrf dG + G+Gae+gi t+klha GP+GLe L+++k
  lcl|NCBI__GCF_000422285.1:WP_028320041.1 357 LGEVDSSVVLVNASTRFNDGNQLGLGAEIGINTSKLHAFGPMGLEELTTTK 407
                                               ************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (418 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: 00:00:00.02
# Mc/sec: 7.55
//
[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