Alignments for a candidate for proA in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Sinorhizobium meliloti 1021

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate SMc03777 SMc03777 gamma-glutamyl phosphate reductase

Query= BRENDA::A7Y114
         (420 letters)



>FitnessBrowser__Smeli:SMc03777
          Length = 427

 Score =  350 bits (897), Expect = e-101
 Identities = 180/424 (42%), Positives = 267/424 (62%), Gaps = 6/424 (1%)

Query: 2   TLTKDNVNVEAQAIE----AKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKD 57
           T+ KD  +V A  +E    AK A++ L   S + K+ AL  +A V+      ILAAN  D
Sbjct: 4   TVEKDK-DVNAMMLEIGRRAKAAARPLATASAERKHAALVAMAGVIVTRTAEILAANALD 62

Query: 58  LRNGREQGFTEAFMDRLSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVT 117
           L N RE G   AF+DRL+L++ RIRD A G+R +AEL DP G+ +S+W   NGL +E+V 
Sbjct: 63  LENARESGVASAFIDRLTLTESRIRDMADGIRAIAELIDPVGEVISEWDRPNGLHIERVR 122

Query: 118 VPLGVIGMIYEARPNVTVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIP 177
            PLGVIG+IYE+RPNVT DA  L LK+GNA++L+GGS + +S++AI   + + L    +P
Sbjct: 123 TPLGVIGVIYESRPNVTADAGALCLKAGNAVILRGGSDSFHSSRAIHACLTEGLKVAGLP 182

Query: 178 QESVQFIASTDRAATNQLFT-MKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIY 236
           ++++Q +   DRAA   + T +   +DV++PRGG  L+  V   A VPV     G CHIY
Sbjct: 183 EDAIQMVPVADRAAVGAMLTGLNGAIDVIVPRGGKSLVARVQNEARVPVFAHLEGLCHIY 242

Query: 237 IDKDADVEKAISILVNAKTDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDE 296
           +D  AD + A  I+VNAK  R  +C AAETL++ ++   + +  L+ AL      V   +
Sbjct: 243 VDASADRDMAKKIVVNAKMRRTGICGAAETLLIDRNAAEKFAKPLLEALVDAGCEVRASD 302

Query: 297 HVLTIIPDAVPAGEDDWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAA 356
            + +++P    A ++DW  EYL   I+ + VD +  AI HI T+ + H+EA++ E+    
Sbjct: 303 DLASVMPGLKAATDEDWATEYLDAIISARLVDGISGAIEHINTWSSAHTEAVIAEDPAVV 362

Query: 357 DKFLAIVDAAAIYHNASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGT 416
           ++F + +D+A + HNAST+F DGG  G G EIGI+T K+HARGP+G+  LT+ K+ ++GT
Sbjct: 363 ERFFSEIDSAILLHNASTQFADGGEFGMGGEIGIATGKMHARGPVGVEQLTSFKYRVRGT 422

Query: 417 GQIR 420
           GQ+R
Sbjct: 423 GQVR 426


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: 498
Number of extensions: 21
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: 427
Length adjustment: 32
Effective length of query: 388
Effective length of database: 395
Effective search space:   153260
Effective search space used:   153260
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 SMc03777 SMc03777 (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.26307.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   8.6e-136  438.8   0.5   9.9e-136  438.6   0.5    1.0  1  lcl|FitnessBrowser__Smeli:SMc03777  SMc03777 gamma-glutamyl phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03777  SMc03777 gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.6   0.5  9.9e-136  9.9e-136       1     398 []      22     416 ..      22     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 438.6 bits;  conditional E-value: 9.9e-136
                           TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdv 75 
                                         ak aa  la+ s++ k+ al ++a  +  ++ +ilaana d+++a+e G+a a++drL+Lte++++++ad+++ +
  lcl|FitnessBrowser__Smeli:SMc03777  22 AKAAARPLATASAERKHAALVAMAGVIVTRTAEILAANALDLENARESGVASAFIDRLTLTESRIRDMADGIRAI 96 
                                         899************************************************************************ PP

                           TIGR00407  76 ieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalvev 150
                                         +eL dPvG+vi++ ++ +GL++ervr+PlGv+gviye+rP+v++d+ +Lclk+GnaviL+Gg+++ +s +a+ + 
  lcl|FitnessBrowser__Smeli:SMc03777  97 AELIDPVGEVISEWDRPNGLHIERVRTPLGVIGVIYESRPNVTADAGALCLKAGNAVILRGGSDSFHSSRAIHAC 171
                                         *************************************************************************** PP

                           TIGR00407 151 iqdaleqtglpveavqliedpdreevkellk.ldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldes 224
                                         + + l+ +glp  a+q++  +dr+ v  +l+ l+  +d+++PrGg++lv  +++e+++Pv+ h +G Chiy+d+s
  lcl|FitnessBrowser__Smeli:SMc03777 172 LTEGLKVAGLPEDAIQMVPVADRAAVGAMLTgLNGAIDVIVPRGGKSLVARVQNEARVPVFAHLEGLCHIYVDAS 246
                                         **************************9999659****************************************** PP

                           TIGR00407 225 adlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevske 299
                                         ad  +akk++v+ak +r   C a etLL++++ ae+f + L ++l ++g e+ra +    +++     + ++++e
  lcl|FitnessBrowser__Smeli:SMc03777 247 ADRDMAKKIVVNAKMRRTGICGAAETLLIDRNAAEKFAKPLLEALVDAGCEVRASDDLASVMPGL---K-AATDE 317
                                         ******************************************************88777777655...3.34579 PP

                           TIGR00407 300 dfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGa 374
                                         d+ +e+l+ ++s+++v+ +  aiehi+++++ h++a+++ed +  e+f  e+dsa   +nast+fadG++fG+G 
  lcl|FitnessBrowser__Smeli:SMc03777 318 DWATEYLDAIISARLVDGISGAIEHINTWSSAHTEAVIAEDPAVVERFFSEIDSAILLHNASTQFADGGEFGMGG 392
                                         *************************************************************************** PP

                           TIGR00407 375 evgistqklharGPvGLeaLvsyk 398
                                         e+gi+t k+harGPvG+e L+s+k
  lcl|FitnessBrowser__Smeli:SMc03777 393 EIGIATGKMHARGPVGVEQLTSFK 416
                                         **********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (427 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: 00:00:00.01
# Mc/sec: 12.53
//
[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