Alignments for a candidate for proA in Methanosarcina mazei Go1

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Methanosarcina mazei Go1

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; GSA dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; EC 1.2.1.41 (characterized)
to candidate WP_011032769.1 MM_RS04290 gamma-glutamyl-phosphate reductase

Query= SwissProt::P54885
         (456 letters)



>NCBI__GCF_000007065.1:WP_011032769.1
          Length = 447

 Score =  342 bits (876), Expect = 2e-98
 Identities = 196/448 (43%), Positives = 282/448 (62%), Gaps = 23/448 (5%)

Query: 11  ARKAGNILKTISNEGRSDILYKIHDALKANAHAIEEANKIDLAVA---KETG-LADSLLK 66
           A+KA   L ++S+E ++  L  + +AL      I EAN  DL  A   K+ G L  +L+ 
Sbjct: 12  AKKASIELASVSSEVKNRALEAMAEALDKERKIILEANLKDLEYAAQLKKAGKLTQALVD 71

Query: 67  RLDLFKGDKFEVMLQGIKDVAELEDPVGKVKMARELDDGLTLYQVTAPVGVLLVIFESRP 126
           RL +    K + M+ GI+DV +L+DPVG+     ELDD L LYQV+ P+G++ VIFESRP
Sbjct: 72  RLKV-TDSKVDGMIAGIRDVIKLKDPVGETLSTLELDDDLILYQVSCPIGLIGVIFESRP 130

Query: 127 EVIANITALSIKSGNAAILKGGKESVNTFREMAKIVNDTIAQFQSETGVPVGSVQLIETR 186
           +V+  + +L +KSGNA I KGG E+  + R +  I+   +   +S  G+P G+ QL+ETR
Sbjct: 131 DVVPQVMSLCLKSGNATIFKGGSEARESNRTIFDIL---VRAIESTGGMPEGAFQLMETR 187

Query: 187 QDVSDLLDQDEYIDLVVPRGSNALVRKIKDTTKIPVLGHADGICSIYLDEDADLIKAKRI 246
           +++  LL  D Y+DL++PRGSN  V+ I+D TKIPVLGH  GIC IY+DE AD   A ++
Sbjct: 188 EEIMSLLSLDAYVDLLIPRGSNEFVKFIQDNTKIPVLGHTSGICHIYVDEFADPDTAWQV 247

Query: 247 SLDAKTNYPAGCNAMETLLINPKFSK-WWEVLENLTLEGGVTIHATKDLKTAYFDK-LNE 304
             DAK  YPA CNA+ETLL+N   ++ +   +  + L+ GV +   +   +   +K L+ 
Sbjct: 248 CFDAKVQYPAVCNAIETLLVNRNIAEVFLPKMAEMYLKAGVELRCDEGSYSLLSEKGLSP 307

Query: 305 LGKLTEAIQCKTVDADEEQDFDKEFLSLDLAAKFVTSTESAIQHINTHSSRHTDAIVTEN 364
           L + T+            +D+  E+  L L+ K V + + A+ HINT  S HTD I+TEN
Sbjct: 308 LSRATD------------EDWSLEYNDLILSIKLVDTIKEAVDHINTFGSHHTDGIITEN 355

Query: 365 KANAEKFMKGVDSSGVYWNASTRFADGFRYGFGAEVGISTSKIHARGPVGLDGLVSYQYQ 424
            +  ++F+  VDSS V  NASTRFADG+RYG GAEVGIST+KIH+RGPVG++GL+ Y+Y 
Sbjct: 356 ASRRKEFIGLVDSSSVMVNASTRFADGYRYGKGAEVGISTNKIHSRGPVGMEGLLIYKYI 415

Query: 425 IRGDGQVASDYLGAGGNKAFVHKDLDIK 452
           + G GQV +DY G    K + H+ LD+K
Sbjct: 416 LMGKGQVVADYAGKNA-KPYTHRKLDLK 442


Lambda     K      H
   0.315    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: 540
Number of extensions: 23
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: 456
Length of database: 447
Length adjustment: 33
Effective length of query: 423
Effective length of database: 414
Effective search space:   175122
Effective search space used:   175122
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_011032769.1 MM_RS04290 (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.25845.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-152  492.8   0.0   3.8e-152  492.6   0.0    1.0  1  lcl|NCBI__GCF_000007065.1:WP_011032769.1  MM_RS04290 gamma-glutamyl-phosph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000007065.1:WP_011032769.1  MM_RS04290 gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.6   0.0  3.8e-152  3.8e-152       1     398 []      12     413 ..      12     413 .. 0.97

  Alignments for each domain:
  == domain 1  score: 492.6 bits;  conditional E-value: 3.8e-152
                                 TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaa...kenG.ladalldrLlLteekl 65 
                                               ak+a+++la++s++ kn+al+++a++L +e ++il+an kd++ a   k+ G l++al+drL++t++k+
  lcl|NCBI__GCF_000007065.1:WP_011032769.1  12 AKKASIELASVSSEVKNRALEAMAEALDKERKIILEANLKDLEYAaqlKKAGkLTQALVDRLKVTDSKV 80 
                                               89****************************************987444334449*************** PP

                                 TIGR00407  66 ksiaddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviL 134
                                                +++++++dvi+L+dPvG+ +++ eld+ L l++v++P+G +gvi+e+rP+v+ +v sLclk+Gna i+
  lcl|NCBI__GCF_000007065.1:WP_011032769.1  81 DGMIAGIRDVIKLKDPVGETLSTLELDDDLILYQVSCPIGLIGVIFESRPDVVPQVMSLCLKSGNATIF 149
                                               ********************************************************************* PP

                                 TIGR00407 135 kGgkeavrsnkalveviqdaleqt.glpveavqliedpdreevkellkldeyvdlliPrGgnelvklik 202
                                               kGg+ea +sn+++ +++ +a+e+t g+p +a ql+e+  ree++ ll+ld yvdlliPrG+ne+vk i+
  lcl|NCBI__GCF_000007065.1:WP_011032769.1 150 KGGSEARESNRTIFDILVRAIESTgGMPEGAFQLMET--REEIMSLLSLDAYVDLLIPRGSNEFVKFIQ 216
                                               **********************9637***********..****************************** PP

                                 TIGR00407 203 eestiPvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqlee 271
                                               ++++iPvl+h+ G+Chiy+de ad   a +v  dak q+P++CnaietLLvn++iae fl+++++   +
  lcl|NCBI__GCF_000007065.1:WP_011032769.1 217 DNTKIPVLGHTSGICHIYVDEFADPDTAWQVCFDAKVQYPAVCNAIETLLVNRNIAEVFLPKMAEMYLK 285
                                               ********************************************************************* PP

                                 TIGR00407 272 kgvelradalvlkllelekate.aevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailte 339
                                               +gvelr d+    ll+ ++++  +++++ed+  e+ +l+Ls+k+v+ ++ea++hi+++g++h+d+i+te
  lcl|NCBI__GCF_000007065.1:WP_011032769.1 286 AGVELRCDEGSYSLLSEKGLSPlSRATDEDWSLEYNDLILSIKLVDTIKEAVDHINTFGSHHTDGIITE 354
                                               **********9999888777651578899**************************************** PP

                                 TIGR00407 340 dkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                               + +  ++f+  vds++v vnastrfadG+r+G Gaevgist+k+h+rGPvG+e+L  yk
  lcl|NCBI__GCF_000007065.1:WP_011032769.1 355 NASRRKEFIGLVDSSSVMVNASTRFADGYRYGKGAEVGISTNKIHSRGPVGMEGLLIYK 413
                                               *******************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (447 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: 00:00:00.02
# Mc/sec: 8.45
//
[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