Aligments for a candidate for argG in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Aligments for a candidate for argG in Azospirillum brasilense Sp245

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate AZOBR_RS00785 AZOBR_RS00785 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__azobra:AZOBR_RS00785
          Length = 411

 Score =  513 bits (1322), Expect = e-150
 Identities = 256/395 (64%), Positives = 305/395 (77%), Gaps = 4/395 (1%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIAL-- 59
           K+VLAYSGGLDTS+ILKWL+ETY+ EV+ FTAD+GQGEE+E AR+KA   G         
Sbjct: 11  KVVLAYSGGLDTSVILKWLQETYQCEVVTFTADLGQGEELEPARKKAELLGIKPENIFID 70

Query: 60  DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119
           DL+EEFVRDFVFPM RA  +YEG YLLGTSIARPLIAK  + IA + GA+A+AHGATGKG
Sbjct: 71  DLREEFVRDFVFPMFRANTLYEGTYLLGTSIARPLIAKRQIEIANQVGADAVAHGATGKG 130

Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQ--EKPYSMDAN 177
           NDQVRFEL  YAL+PDIK+IAPWREW    R  +I YAE + IP+   +  E PYS DAN
Sbjct: 131 NDQVRFELGYYALRPDIKIIAPWREWDLSSRTRLIDYAEKNQIPIAKDKRGEAPYSTDAN 190

Query: 178 LLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAA 237
           LLHISYEG  LEDPW EP + M+  +  PE+APD P YVEVEF  GD VA++G+ LSPAA
Sbjct: 191 LLHISYEGKALEDPWVEPFEDMYTRSVAPEKAPDTPTYVEVEFKRGDAVAIDGKALSPAA 250

Query: 238 LLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQ 297
           LL  LN +GG +G+GR+D+VENR+VGMKSRGVYETPGGTIL  A RA+ES+TLDR   H 
Sbjct: 251 LLTELNRLGGENGIGRLDLVENRYVGMKSRGVYETPGGTILLAAHRAMESITLDRGAGHL 310

Query: 298 RDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSL 357
           +D L P+YAEL+Y G+W++PER ALQA  D     V GV RLKL+KGNV VVGRK+P SL
Sbjct: 311 KDELMPRYAELIYCGYWFSPERLALQALIDQTQEPVNGVVRLKLFKGNVTVVGRKSPNSL 370

Query: 358 YRQDLVSFDEAGGYDQKDAEGFIKIQALRLRVRAL 392
           YR D V+F+E   Y+QKDAEGFIK+ ALRLR+ A+
Sbjct: 371 YRMDYVTFEEDSVYNQKDAEGFIKLNALRLRLGAM 405


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: 507
Number of extensions: 11
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 400
Length of database: 411
Length adjustment: 31
Effective length of query: 369
Effective length of database: 380
Effective search space:   140220
Effective search space used:   140220
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 AZOBR_RS00785 AZOBR_RS00785 (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.16586.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-145  471.9   0.0   1.2e-145  471.7   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS00785  AZOBR_RS00785 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS00785  AZOBR_RS00785 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  471.7   0.0  1.2e-145  1.2e-145       1     387 [.      11     401 ..      11     407 .. 0.97

  Alignments for each domain:
  == domain 1  score: 471.7 bits;  conditional E-value: 1.2e-145
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGae..kayviDareefvk 66 
                                               kvvlaysGGlDtsv+lk+l+e   +ev+++t+d+Gq+ e+l+ +++ka  lG +  +  + D reefv+
  lcl|FitnessBrowser__azobra:AZOBR_RS00785  11 KVVLAYSGGLDTSVILKWLQETyQCEVVTFTADLGQG-EELEPARKKAELLGIKpeNIFIDDLREEFVR 78 
                                               8*********************899***********9.9************986214555589****** PP

                                 TIGR00032  67 dylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdl 135
                                               d++f+  +an++yeg+Yll+t++aRpliak+++e+a++ ga+avahG+tgKGnDqvRFel  ++l+pd+
  lcl|FitnessBrowser__azobra:AZOBR_RS00785  79 DFVFPMFRANTLYEGTYLLGTSIARPLIAKRQIEIANQVGADAVAHGATGKGNDQVRFELGYYALRPDI 147
                                               ********************************************************************* PP

                                 TIGR00032 136 kviaPvreleli.ReeeieyaaekGievpvek..ekaysiDenllgrsiEageLEdpsteppediyelv 201
                                               k+iaP+re++l+ R+ +i+ya+++ i+++ +k  e +ys+D nll++s+E++ LEdp++ep ed+y+  
  lcl|FitnessBrowser__azobra:AZOBR_RS00785 148 KIIAPWREWDLSsRTRLIDYAEKNQIPIAKDKrgEAPYSTDANLLHISYEGKALEDPWVEPFEDMYTRS 216
                                               ***********99***************99875579********************************9 PP

                                 TIGR00032 202 kdpiektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYE 270
                                               + p++++ d+p +ve+eF++G  va++g+ l+p  l+ ++n+++g++G+Gr+D vE+R++g+KsR++YE
  lcl|FitnessBrowser__azobra:AZOBR_RS00785 217 VAPEKAP-DTPTYVEVEFKRGDAVAIDGKALSPAALLTELNRLGGENGIGRLDLVENRYVGMKSRGVYE 284
                                               9777776.************************************************************* PP

                                 TIGR00032 271 apalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvk 339
                                               +p+ ++L+ Ah+++e+ +l++   ++k+    +y+eliY G+wf+p++ al+ali++tqe v+G+vr+k
  lcl|FitnessBrowser__azobra:AZOBR_RS00785 285 TPGGTILLAAHRAMESITLDRGAGHLKDELMPRYAELIYCGYWFSPERLALQALIDQTQEPVNGVVRLK 353
                                               ********************************************************************* PP

                                 TIGR00032 340 lfkGnaivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqik 387
                                               lfkGn++v+grks++slY  + v+fe+d+ ++qkda+Gfik+++l+ +
  lcl|FitnessBrowser__azobra:AZOBR_RS00785 354 LFKGNVTVVGRKSPNSLYRMDYVTFEEDSVYNQKDAEGFIKLNALRLR 401
                                               ********************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (411 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: 8.76
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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