Alignments for a candidate for argG in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Magnetospirillum magneticum AMB-1

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_011383538.1 AMB_RS05720 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>NCBI__GCF_000009985.1:WP_011383538.1
          Length = 404

 Score =  503 bits (1296), Expect = e-147
 Identities = 248/392 (63%), Positives = 305/392 (77%), Gaps = 4/392 (1%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIAL-- 59
           K+VLAYSGGLDTSIIL+WL++ Y+ EV+ FTAD+GQGEE+E AR KA   G  +      
Sbjct: 7   KVVLAYSGGLDTSIILRWLQDQYQCEVVTFTADLGQGEELEPARAKARLMGIKEENIFID 66

Query: 60  DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119
           DL+EEFVRDFVFPM RA A+YEG YLLGTSIARPLI+K  + IA   GA+A++HGATGKG
Sbjct: 67  DLREEFVRDFVFPMFRANALYEGVYLLGTSIARPLISKRQIEIANMVGADAVSHGATGKG 126

Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQ--EKPYSMDAN 177
           NDQVRFE+  YALKPDIKVIAPWR W    R +++ +AE H IP+   +  E PYS DAN
Sbjct: 127 NDQVRFEMGYYALKPDIKVIAPWRLWDLTSRTKLLDFAEKHQIPIAKDKRGEAPYSTDAN 186

Query: 178 LLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAA 237
           LLHISYEG  LEDPW EP + M+  +  PE APD P Y+E+EF +GD VA++G RLSPAA
Sbjct: 187 LLHISYEGKALEDPWVEPFEDMYTRSVAPENAPDKPTYIEIEFEKGDAVAIDGVRLSPAA 246

Query: 238 LLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQ 297
           LL +LNE+GG +G+GR+D+VENRFVGMKSRGVYETPGG++L  A RA+ESLTLDR   H 
Sbjct: 247 LLTKLNELGGANGIGRLDLVENRFVGMKSRGVYETPGGSVLIVAHRAMESLTLDRGESHL 306

Query: 298 RDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSL 357
           +D L P+YAEL+Y GFW+APER A+Q   D V+ +V+G  RLKL+KG   VVGRK+PKSL
Sbjct: 307 KDELMPRYAELIYNGFWFAPERIAIQTMIDKVSENVSGTVRLKLFKGVASVVGRKSPKSL 366

Query: 358 YRQDLVSFDEAGGYDQKDAEGFIKIQALRLRV 389
           YR D V+F+E   YDQ+DA+GFIK+ ALR+R+
Sbjct: 367 YRMDYVTFEEDSVYDQRDAQGFIKLNALRMRL 398


Lambda     K      H
   0.319    0.137    0.402 

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: 493
Number of extensions: 15
Number of successful extensions: 3
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: 400
Length of database: 404
Length adjustment: 31
Effective length of query: 369
Effective length of database: 373
Effective search space:   137637
Effective search space used:   137637
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_011383538.1 AMB_RS05720 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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/TIGR00032.hmm
# target sequence database:        /tmp/gapView.15703.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-144  468.1   0.0   1.8e-144  467.8   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011383538.1  AMB_RS05720 argininosuccinate sy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011383538.1  AMB_RS05720 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.8   0.0  1.8e-144  1.8e-144       1     390 [.       7     400 ..       7     403 .. 0.96

  Alignments for each domain:
  == domain 1  score: 467.8 bits;  conditional E-value: 1.8e-144
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaeka.yvi.Dareefvk 66 
                                               kvvlaysGGlDts++l++l+++  +ev+++t+d+Gq+ e+l+ ++ ka  +G ++  + i D reefv+
  lcl|NCBI__GCF_000009985.1:WP_011383538.1   7 KVVLAYSGGLDTSIILRWLQDQyQCEVVTFTADLGQG-EELEPARAKARLMGIKEEnIFIdDLREEFVR 74 
                                               8*********************999***********9.99********999976541344379****** PP

                                 TIGR00032  67 dylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdl 135
                                               d++f+  +ana+yeg+Yll+t++aRpli+k+++e+a+  ga+av+hG+tgKGnDqvRFe+  ++l+pd+
  lcl|NCBI__GCF_000009985.1:WP_011383538.1  75 DFVFPMFRANALYEGVYLLGTSIARPLISKRQIEIANMVGADAVSHGATGKGNDQVRFEMGYYALKPDI 143
                                               ********************************************************************* PP

                                 TIGR00032 136 kviaPvreleli.ReeeieyaaekGievpvek..ekaysiDenllgrsiEageLEdpsteppediyelv 201
                                               kviaP+r ++l+ R++++++a+++ i+++ +k  e +ys+D nll++s+E++ LEdp++ep ed+y+  
  lcl|NCBI__GCF_000009985.1:WP_011383538.1 144 KVIAPWRLWDLTsRTKLLDFAEKHQIPIAKDKrgEAPYSTDANLLHISYEGKALEDPWVEPFEDMYTRS 212
                                               ***********99***************99875579********************************9 PP

                                 TIGR00032 202 kdpiektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYE 270
                                               + p++++ d+p ++eieFekG  va++g++l+p  l+ k+ne++g++G+Gr+D vE+R +g+KsR++YE
  lcl|NCBI__GCF_000009985.1:WP_011383538.1 213 VAPENAP-DKPTYIEIEFEKGDAVAIDGVRLSPAALLTKLNELGGANGIGRLDLVENRFVGMKSRGVYE 280
                                               9787777.************************************************************* PP

                                 TIGR00032 271 apalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvk 339
                                               +p+  +Li Ah+++e+l+l++ + ++k+    +y+eliY+G+wf p++ a++++i+k+ e+v+Gtvr+k
  lcl|NCBI__GCF_000009985.1:WP_011383538.1 281 TPGGSVLIVAHRAMESLTLDRGESHLKDELMPRYAELIYNGFWFAPERIAIQTMIDKVSENVSGTVRLK 349
                                               ********************************************************************* PP

                                 TIGR00032 340 lfkGnaivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqikvyr 390
                                               lfkG a v+grks++slY  + v+fe+d+ +dq+da+Gfik+++l+++  +
  lcl|NCBI__GCF_000009985.1:WP_011383538.1 350 LFKGVASVVGRKSPKSLYRMDYVTFEEDSVYDQRDAQGFIKLNALRMRLAK 400
                                               *********************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (404 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: 00:00:00.01
# Mc/sec: 8.29
//
[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