Alignments for a candidate for argG in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Marinobacter adhaerens HP15

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate GFF2423 HP15_2367 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__Marino:GFF2423
          Length = 408

 Score =  504 bits (1299), Expect = e-147
 Identities = 246/392 (62%), Positives = 304/392 (77%), Gaps = 2/392 (0%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61
           K+VLAYSGGLDTS+I++WL++TY  EV+ FTADIGQGEEVE AR KA   G  +    DL
Sbjct: 11  KVVLAYSGGLDTSVIVRWLQDTYNCEVVTFTADIGQGEEVEPARAKAEALGVKEIYIEDL 70

Query: 62  KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121
           +EEFVRD+VFPM RA  +YEG YLLGTSIARPLIAK L+ IA E GA+AI+HGATGKGND
Sbjct: 71  REEFVRDYVFPMFRANTIYEGEYLLGTSIARPLIAKRLIDIANETGADAISHGATGKGND 130

Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEK-PYSMDANLLH 180
           QVRFEL AYALKP +KVIAPWREW    R++++ Y E   IPV + + K PYSMDANLLH
Sbjct: 131 QVRFELGAYALKPGVKVIAPWREWDLNSREKLLKYCEERNIPVEMKKGKSPYSMDANLLH 190

Query: 181 ISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQ 240
           ISYEG  LEDPWAE  + M+R +  PE APD P YVE+ + +GD VA++G+ + P  +L+
Sbjct: 191 ISYEGINLEDPWAEAEEDMWRWSVSPEAAPDEPTYVELTYKKGDIVAIDGQDMKPHLVLE 250

Query: 241 RLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDM 300
            LN++ G +G+GR+DIVENR+VGMKSRG YETPGGTI+  A RA+ES+TLDREV H +D 
Sbjct: 251 TLNKLAGANGIGRLDIVENRYVGMKSRGCYETPGGTIMLRAHRAIESITLDREVAHLKDS 310

Query: 301 LSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQ 360
           + P+YAE++Y G+W++PEREALQA  D     V G  RLKLYKGNV VVGRK+  SL+ +
Sbjct: 311 IMPRYAEVIYNGYWWSPEREALQALIDQTQNYVNGTVRLKLYKGNVDVVGRKSEDSLFDE 370

Query: 361 DLVSFDE-AGGYDQKDAEGFIKIQALRLRVRA 391
            + +F+E  G YDQKDAEGFIK+ ALRLR+ A
Sbjct: 371 KIATFEEDQGAYDQKDAEGFIKLNALRLRIAA 402


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: 517
Number of extensions: 14
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: 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 GFF2423 HP15_2367 (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.17439.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.2e-146  473.6   0.0   3.7e-146  473.4   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF2423  HP15_2367 argininosuccinate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2423  HP15_2367 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.4   0.0  3.7e-146  3.7e-146       1     389 [.      11     401 ..      11     406 .. 0.98

  Alignments for each domain:
  == domain 1  score: 473.4 bits;  conditional E-value: 3.7e-146
                           TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaaiq 74 
                                         kvvlaysGGlDtsv++++l++  ++ev+++t+d+Gq+ e+++ ++ ka +lG+++ y+ D reefv+dy+f+  +
  lcl|FitnessBrowser__Marino:GFF2423  11 KVVLAYSGGLDTSVIVRWLQDTyNCEVVTFTADIGQG-EEVEPARAKAEALGVKEIYIEDLREEFVRDYVFPMFR 84 
                                         8*********************99************9.9************************************ PP

                           TIGR00032  75 anavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvreleli.R 148
                                         an++yeg+Yll+t++aRpliak+l+++a++ ga+a++hG+tgKGnDqvRFel  ++l+p +kviaP+re++l  R
  lcl|FitnessBrowser__Marino:GFF2423  85 ANTIYEGEYLLGTSIARPLIAKRLIDIANETGADAISHGATGKGNDQVRFELGAYALKPGVKVIAPWREWDLNsR 159
                                         ************************************************************************88* PP

                           TIGR00032 149 eeeieyaaekGievpvekek.aysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieFekG 222
                                         e++++y +e+ i+v+++k k +ys+D nll++s+E+ +LEdp++e  ed++++ ++p++++ dep +ve++++kG
  lcl|FitnessBrowser__Marino:GFF2423 160 EKLLKYCEERNIPVEMKKGKsPYSMDANLLHISYEGINLEDPWAEAEEDMWRWSVSPEAAP-DEPTYVELTYKKG 233
                                         ****************996439*********************************888887.************* PP

                           TIGR00032 223 vPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefk 297
                                           va++g+ ++p  +++++n++ag++G+Gr+DivE+R++g+KsR++YE+p+ +++++Ah+++e+ +l+++v+++k
  lcl|FitnessBrowser__Marino:GFF2423 234 DIVAIDGQDMKPHLVLETLNKLAGANGIGRLDIVENRYVGMKSRGCYETPGGTIMLRAHRAIESITLDREVAHLK 308
                                         *************************************************************************** PP

                           TIGR00032 298 eiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfek.dkefd 371
                                         + +  +y+e+iY+G+w++p++eal+ali++tq+ v+Gtvr+kl+kGn+ v+grkse+sl+de++++fe+ + ++d
  lcl|FitnessBrowser__Marino:GFF2423 309 DSIMPRYAEVIYNGYWWSPEREALQALIDQTQNYVNGTVRLKLYKGNVDVVGRKSEDSLFDEKIATFEEdQGAYD 383
                                         ********************************************************************955689* PP

                           TIGR00032 372 qkdaiGfikirglqikvy 389
                                         qkda+Gfik+++l+ ++ 
  lcl|FitnessBrowser__Marino:GFF2423 384 QKDAEGFIKLNALRLRIA 401
                                         *************98876 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: 7.39
//
[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