Alignments for a candidate for proA in Mesorhizobium ciceri WSM1271

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Mesorhizobium ciceri WSM1271

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate YP_004140424.1 Mesci_1211 gamma-glutamyl phosphate reductase

Query= BRENDA::A7Y114
         (420 letters)



>NCBI__GCF_000185905.1:YP_004140424.1
          Length = 428

 Score =  358 bits (920), Expect = e-103
 Identities = 181/405 (44%), Positives = 262/405 (64%), Gaps = 1/405 (0%)

Query: 17  AKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEAFMDRLSL 76
           A+ A++ L I +   KN AL  +A+ +    + IL AN  D+ NG E G + +FMDRL L
Sbjct: 23  ARAAARPLAIATTAAKNAALLAMAEAIVAREQDILDANAIDVSNGHESGLSTSFMDRLKL 82

Query: 77  SQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEARPNVTVD 136
              RIR  A G+R++A L DP G  ++ W   NGL +E+V  PLGV+G+IYE+RPNVT D
Sbjct: 83  DPARIRAMADGIREIAALRDPVGDVIAQWDRPNGLHIERVRTPLGVVGVIYESRPNVTAD 142

Query: 137 ATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDRAATNQLF 196
           A  L LK+GN ++L+GGS ++NS+ AI   + + L +  +P++++Q + +TDRAA  ++ 
Sbjct: 143 AGALCLKAGNPVILRGGSDSLNSSAAIHACLVEGLKQAGLPEDAIQLVPTTDRAAVGEML 202

Query: 197 T-MKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISILVNAKT 255
             +  ++DV+IPRGG  L+  V   A VPV     G CH+YID+ A ++ A+ I VNAK 
Sbjct: 203 KGLGGNLDVIIPRGGKSLVGRVQAEARVPVFAHLEGICHLYIDRSAKLDMAVRIAVNAKM 262

Query: 256 DRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAVPAGEDDWKN 315
            R  VC AAETL+V +   + H   ++ AL+     +H D  VL +  DA PA + DW  
Sbjct: 263 RRTGVCGAAETLLVDRAVASTHLVPILDALRAAGCEIHADAEVLKVFFDAKPATDADWVT 322

Query: 316 EYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAIYHNASTR 375
           EYL   IAVK VD +  AI HIET+ + H+EAIV E+ +A ++F   +D+A + HNAST+
Sbjct: 323 EYLDAIIAVKLVDGIGGAIEHIETFSSHHTEAIVAEDAQAVERFFNEIDSAILLHNASTQ 382

Query: 376 FTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420
           F DGG  G GAEIGI+T K+HARGP+G+  LT+ K+ ++G+GQ+R
Sbjct: 383 FADGGEFGMGAEIGIATGKMHARGPVGVEQLTSFKYRVRGSGQVR 427


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: 484
Number of extensions: 20
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: 428
Length adjustment: 32
Effective length of query: 388
Effective length of database: 396
Effective search space:   153648
Effective search space used:   153648
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 YP_004140424.1 Mesci_1211 (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.19481.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-138  448.3   0.5   1.3e-138  448.1   0.5    1.0  1  lcl|NCBI__GCF_000185905.1:YP_004140424.1  Mesci_1211 gamma-glutamyl phosph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004140424.1  Mesci_1211 gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.1   0.5  1.3e-138  1.3e-138       1     398 []      23     417 ..      23     417 .. 0.98

  Alignments for each domain:
  == domain 1  score: 448.1 bits;  conditional E-value: 1.3e-138
                                 TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 
                                               a+ aa  la  +ta kn al ++a+++ a+ + il+ana+d+ +++e Gl+ +++drL+L+ ++++ +a
  lcl|NCBI__GCF_000185905.1:YP_004140424.1  23 ARAAARPLAIATTAAKNAALLAMAEAIVAREQDILDANAIDVSNGHESGLSTSFMDRLKLDPARIRAMA 91 
                                               899****************************************************************** PP

                                 TIGR00407  70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138
                                               d++++++ L dPvG+vi + ++ +GL++ervr+PlGv+gviye+rP+v++d+ +Lclk+Gn viL+Gg+
  lcl|NCBI__GCF_000185905.1:YP_004140424.1  92 DGIREIAALRDPVGDVIAQWDRPNGLHIERVRTPLGVVGVIYESRPNVTADAGALCLKAGNPVILRGGS 160
                                               ********************************************************************* PP

                                 TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellk.ldeyvdlliPrGgnelvklikeest 206
                                               ++ +s +a+ + + + l+q+glp  a+ql+ ++dr+ v e+lk l   +d++iPrGg++lv  ++ e++
  lcl|NCBI__GCF_000185905.1:YP_004140424.1 161 DSLNSSAAIHACLVEGLKQAGLPEDAIQLVPTTDRAAVGEMLKgLGGNLDVIIPRGGKSLVGRVQAEAR 229
                                               ******************************************758999********************* PP

                                 TIGR00407 207 iPvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgve 275
                                               +Pv+ h +G+Ch+y+d+sa+l +a ++ v+ak +r  +C a etLLv++a+a+ +l  + ++l ++g e
  lcl|NCBI__GCF_000185905.1:YP_004140424.1 230 VPVFAHLEGICHLYIDRSAKLDMAVRIAVNAKMRRTGVCGAAETLLVDRAVASTHLVPILDALRAAGCE 298
                                               ********************************************************************* PP

                                 TIGR00407 276 lradalvlkll.elekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkkn 343
                                               ++ada vlk+  ++++at+      d+ +e+l+ +++vk+v+ +  aiehi++++++h++ai++ed ++
  lcl|NCBI__GCF_000185905.1:YP_004140424.1 299 IHADAEVLKVFfDAKPATD-----ADWVTEYLDAIIAVKLVDGIGGAIEHIETFSSHHTEAIVAEDAQA 362
                                               ******9998625555555.....57779**************************************** PP

                                 TIGR00407 344 aekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                                e+f +e+dsa   +nast+fadG++fG+Gae+gi+t k+harGPvG+e L+s+k
  lcl|NCBI__GCF_000185905.1:YP_004140424.1 363 VERFFNEIDSAILLHNASTQFADGGEFGMGAEIGIATGKMHARGPVGVEQLTSFK 417
                                               *****************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (428 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: 13.16
//
[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