Alignments for a candidate for proA in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Pedobacter sp. GW460-11-11-14-LB5

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate CA265_RS20850 CA265_RS20850 glutamate-5-semialdehyde dehydrogenase

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__Pedo557:CA265_RS20850
          Length = 415

 Score =  330 bits (847), Expect = 4e-95
 Identities = 182/410 (44%), Positives = 259/410 (63%), Gaps = 7/410 (1%)

Query: 9   AKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEAMLDRLAL 68
           A+QAS  L  LS    + VL  +A  L A +E+IL  N +D+A      + +   DRL L
Sbjct: 10  AQQASRTLISLSKETTDAVLTALAAALVANTELILAENGKDLAKMP---IEDPKYDRLKL 66

Query: 69  TPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEARPNVTVD 128
           +  R+  IA+D++ V  L+ P+G++I    L++ L +++  VPLGV+GVIYEARPNVT D
Sbjct: 67  SRERIADIANDLKNVAGLSSPLGKIISDKTLENQLHIQKVSVPLGVVGVIYEARPNVTAD 126

Query: 129 VASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDRALVSEML 188
           V SLC KTGN  +L+GG +   +N A   VI   L   G+ A  +  +   +RA    +L
Sbjct: 127 VFSLCFKTGNVAVLKGGSDAEFSNLAIAKVIHGVLDKNGINADILTLLP-AERAATEALL 185

Query: 189 RMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKVIVNAKTQ 248
               ++D+LIPRG   L    RE S IPVI  G G+ H Y DE+ ++ +   +I NAKT+
Sbjct: 186 NARGFVDVLIPRGSQSLINYVRENSKIPVIETGAGIVHTYFDETGDLEKGKAIIFNAKTR 245

Query: 249 RPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAG-PAKVV-AVKA 306
           R S CN+++ +L+N+N     LPAL   +A+  V L+AD  +   L+   PA+++     
Sbjct: 246 RVSVCNSLDCVLINQNRLTD-LPALLSPLADGNVELYADEKSYEALKVSYPAQLLNQASP 304

Query: 307 EEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDSSAVYV 366
           E +  EFLSL L VKIV+DL +A+ HI ++ ++HS+AI++ D  N  +F+NEVD++AVY 
Sbjct: 305 EHFGTEFLSLKLAVKIVADLTEALNHIADYSSKHSEAIISEDADNIAQFLNEVDAAAVYA 364

Query: 367 NASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           NAST FTDG QFGLGAE+ +STQKLHARGPMGLE LT+YKW+  GD  +R
Sbjct: 365 NASTGFTDGAQFGLGAEIGISTQKLHARGPMGLEELTSYKWVVRGDGQVR 414


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: 465
Number of extensions: 23
Number of successful extensions: 5
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: 415
Length adjustment: 31
Effective length of query: 386
Effective length of database: 384
Effective search space:   148224
Effective search space used:   148224
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 CA265_RS20850 CA265_RS20850 (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.724.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.1e-134  435.2   1.6   1.2e-134  435.0   1.6    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS20850  CA265_RS20850 glutamate-5-semial


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS20850  CA265_RS20850 glutamate-5-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.0   1.6  1.2e-134  1.2e-134       1     398 []      10     404 ..      10     404 .. 0.97

  Alignments for each domain:
  == domain 1  score: 435.0 bits;  conditional E-value: 1.2e-134
                                  TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksi 68 
                                                a++a+ +l++ls++  + +l+++a +L a++elila+n kd+a+   + + d+ +drL+L++e++ +i
  lcl|FitnessBrowser__Pedo557:CA265_RS20850  10 AQQASRTLISLSKETTDAVLTALAAALVANTELILAENGKDLAK---MPIEDPKYDRLKLSRERIADI 74 
                                                79****************************************85...89******************* PP

                                  TIGR00407  69 addvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkG 136
                                                a+d+k+v+ L+ P+Gk+i+ ++l++ L++++v+vPlGv+gviyearP+v++dv sLc+ktGn ++LkG
  lcl|FitnessBrowser__Pedo557:CA265_RS20850  75 ANDLKNVAGLSSPLGKIISDKTLENQLHIQKVSVPLGVVGVIYEARPNVTADVFSLCFKTGNVAVLKG 142
                                                ******************************************************************** PP

                                  TIGR00407 137 gkeavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikee 204
                                                g++a +sn a+++vi+  l++ g+ +  + l+   +r+  + ll+   +vd+liPrG+++l+++++e+
  lcl|FitnessBrowser__Pedo557:CA265_RS20850 143 GSDAEFSNLAIAKVIHGVLDKNGINADILTLLPA-ERAATEALLNARGFVDVLIPRGSQSLINYVREN 209
                                                *******************************998.9******************************** PP

                                  TIGR00407 205 stiPvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleek 272
                                                s+iPv+e+++G+ h+y de+ dl+k k +i +akt+r s+Cn+++ +L+n++     l++L + l+++
  lcl|FitnessBrowser__Pedo557:CA265_RS20850 210 SKIPVIETGAGIVHTYFDETGDLEKGKAIIFNAKTRRVSVCNSLDCVLINQNRL-TDLPALLSPLADG 276
                                                ***************************************************988.679********** PP

                                  TIGR00407 273 gvelradalvlkllele.katea.evskedfdkeflsldLsvkivedleeaiehirqygtkhsdailt 338
                                                +vel ad++  + l+++ +a+   ++s e+f +eflsl+L+vkiv dl ea++hi +y++khs+ai++
  lcl|FitnessBrowser__Pedo557:CA265_RS20850 277 NVELYADEKSYEALKVSyPAQLLnQASPEHFGTEFLSLKLAVKIVADLTEALNHIADYSSKHSEAIIS 344
                                                ******998887776652555441556689************************************** PP

                                  TIGR00407 339 edkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                                ed  n  +f++evd+aavy nast f+dG +fG+Gae+gistqklharGP+GLe L+syk
  lcl|FitnessBrowser__Pedo557:CA265_RS20850 345 EDADNIAQFLNEVDAAAVYANASTGFTDGAQFGLGAEIGISTQKLHARGPMGLEELTSYK 404
                                                ***********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (415 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.65
//
[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