Alignments for a candidate for argG in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Phaeobacter inhibens BS107

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate GFF3439 PGA1_c34920 argininosuccinate synthase ArgG

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__Phaeo:GFF3439
          Length = 408

 Score =  491 bits (1263), Expect = e-143
 Identities = 246/399 (61%), Positives = 300/399 (75%), Gaps = 5/399 (1%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGAS--KAIAL 59
           K+VLAYSGGLDTSIILKWL+  Y  EV+ FTAD+GQGEE+E AR+KA   G         
Sbjct: 6   KVVLAYSGGLDTSIILKWLQTEYGCEVVTFTADLGQGEELEPARQKAELLGIKPENIFIE 65

Query: 60  DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119
           D++EEFVRDFVFPM RA AVYEG YLLGTSIARPLI+K LV IAE  GA+A+AHGATGKG
Sbjct: 66  DVREEFVRDFVFPMFRANAVYEGLYLLGTSIARPLISKRLVEIAEATGADAVAHGATGKG 125

Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQ--EKPYSMDAN 177
           NDQVRFEL AYAL PDIKVIAPWREW    R  ++ +AEAH IPV   +  E P+S+DAN
Sbjct: 126 NDQVRFELAAYALNPDIKVIAPWREWDLTSRTRLLEFAEAHQIPVAKDKRGEAPFSVDAN 185

Query: 178 LLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAA 237
           LLH S EG VLEDP    P  +++ T  PE+AP+  E++E+ F +GD V++NGE +SPA 
Sbjct: 186 LLHTSSEGKVLEDPAVAAPDYVYQRTVHPEDAPNEAEFIEIGFEKGDAVSINGEAMSPAT 245

Query: 238 LLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQ 297
           +L +LNE GG+HG+GR+D+VE RFVGMKSRG+YETPGGTIL  A R +ES+T+DR  +H 
Sbjct: 246 ILTQLNEYGGKHGIGRLDLVEGRFVGMKSRGIYETPGGTILLEAHRGIESITMDRGAMHL 305

Query: 298 RDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSL 357
           +D L P+YAEL+Y GFWY+PERE LQA  D     VTG  R+KLYKG+   VGR +  SL
Sbjct: 306 KDQLMPQYAELIYNGFWYSPEREMLQAAIDRSQEHVTGTVRVKLYKGSATTVGRWSDHSL 365

Query: 358 YRQDLVSF-DEAGGYDQKDAEGFIKIQALRLRVRALVER 395
           Y +  V+F D+AG YDQKDA GFI++ ALRL++ A  ER
Sbjct: 366 YSEAHVTFEDDAGAYDQKDAAGFIQLNALRLKLLAARER 404


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: 514
Number of extensions: 18
Number of successful extensions: 4
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: 408
Length adjustment: 31
Effective length of query: 369
Effective length of database: 377
Effective search space:   139113
Effective search space used:   139113
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 GFF3439 PGA1_c34920 (argininosuccinate synthase ArgG)
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.32524.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.4e-145  469.8   0.0   5.1e-145  469.6   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3439  PGA1_c34920 argininosuccinate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3439  PGA1_c34920 argininosuccinate synthase ArgG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.6   0.0  5.1e-145  5.1e-145       1     390 [.       6     400 ..       6     404 .. 0.97

  Alignments for each domain:
  == domain 1  score: 469.6 bits;  conditional E-value: 5.1e-145
                          TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGa..ekayviDareefvkdylfaai 73 
                                        kvvlaysGGlDts++lk+l+ + g+ev+++t+d+Gq+ e+l+ +++ka  lG   e+  + D reefv+d++f+  
  lcl|FitnessBrowser__Phaeo:GFF3439   6 KVVLAYSGGLDTSIILKWLQTEyGCEVVTFTADLGQG-EELEPARQKAELLGIkpENIFIEDVREEFVRDFVFPMF 80 
                                        8*********************9*************9.9***********99722566777*************** PP

                          TIGR00032  74 qanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvreleli.R 148
                                        +anavyeg Yll+t++aRpli+k+lve+a+  ga+avahG+tgKGnDqvRFel  ++lnpd+kviaP+re++l+ R
  lcl|FitnessBrowser__Phaeo:GFF3439  81 RANAVYEGLYLLGTSIARPLISKRLVEIAEATGADAVAHGATGKGNDQVRFELAAYALNPDIKVIAPWREWDLTsR 156
                                        *************************************************************************99* PP

                          TIGR00032 149 eeeieyaaekGievpvek..ekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieFekG 222
                                        + ++e+a+++ i+v+ +k  e ++s+D nll+ s E++ LEdp ++ p+ +y+ +++p++++ +e+e +ei+FekG
  lcl|FitnessBrowser__Phaeo:GFF3439 157 TRLLEFAEAHQIPVAKDKrgEAPFSVDANLLHTSSEGKVLEDPAVAAPDYVYQRTVHPEDAP-NEAEFIEIGFEKG 231
                                        **************99875579**********************************998888.999********** PP

                          TIGR00032 223 vPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefke 298
                                          v++nge ++p +++ ++ne +gkhG+Gr+D vE R +g+KsR+iYE+p+ ++L++Ah+ +e+ ++++  +++k+
  lcl|FitnessBrowser__Phaeo:GFF3439 232 DAVSINGEAMSPATILTQLNEYGGKHGIGRLDLVEGRFVGMKSRGIYETPGGTILLEAHRGIESITMDRGAMHLKD 307
                                        **************************************************************************** PP

                          TIGR00032 299 iveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfek.dkefdqk 373
                                            +y+eliY+G+w++p++e+l+a+i+++qe+vtGtvrvkl+kG+a+++gr s++slY+e  v+fe    ++dqk
  lcl|FitnessBrowser__Phaeo:GFF3439 308 QLMPQYAELIYNGFWYSPEREMLQAAIDRSQEHVTGTVRVKLYKGSATTVGRWSDHSLYSEAHVTFEDdAGAYDQK 383
                                        *******************************************************************944589*** PP

                          TIGR00032 374 daiGfikirglqikvyr 390
                                        da+Gfi++++l+ k  +
  lcl|FitnessBrowser__Phaeo:GFF3439 384 DAAGFIQLNALRLKLLA 400
                                        ***********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (408 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: 00:00:00.02
# Mc/sec: 7.61
//
[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