Alignments for a candidate for argG in Chlorobaculum parvum NCIB 8327

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Chlorobaculum parvum NCIB 8327

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_012502227.1 CPAR_RS05030 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>NCBI__GCF_000020505.1:WP_012502227.1
          Length = 401

 Score =  392 bits (1006), Expect = e-113
 Identities = 189/388 (48%), Positives = 269/388 (69%), Gaps = 1/388 (0%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYR-AEVIAFTADIGQGEEVEEAREKALRTGASKAIALD 60
           KI +AYSGGLDTS+++KWLK+ Y  AE++A T ++GQ  EV+    KAL TGA+    +D
Sbjct: 5   KIAVAYSGGLDTSVMIKWLKDKYEGAEIVAVTGNLGQKMEVDNLEPKALATGAASFHFVD 64

Query: 61  LKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGN 120
           L++ FV D ++  ++AGA+YE  Y L T++ RP++AK LV +A  EG   + HG TGKGN
Sbjct: 65  LRKTFVEDCIWKALKAGALYEDVYPLATALGRPILAKALVDVALAEGCTMLTHGCTGKGN 124

Query: 121 DQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLH 180
           DQVRFE+T  +L P +KV+AP REW F  R++ I YA  H IPV  T++ PYS+D N+  
Sbjct: 125 DQVRFEVTFASLAPHMKVVAPLREWEFTSREQEITYALEHNIPVSATKKNPYSIDENIWG 184

Query: 181 ISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQ 240
           IS E GVLEDP   PP   +++T  PEEAPD P  V+++F EG PVA++G+++    L+ 
Sbjct: 185 ISIECGVLEDPMVPPPADAYQITTSPEEAPDKPTVVDIDFVEGIPVALDGQQMEGLDLIV 244

Query: 241 RLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDM 300
           +LNE+G  +GVGR+D++ENR VG+KSR +YE P  TIL+ A R +E LTL++ V   +  
Sbjct: 245 KLNELGAMNGVGRLDMIENRVVGIKSREIYEAPAATILHFAHRELERLTLEKSVFQYKRN 304

Query: 301 LSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQ 360
           +   YA ++Y G W++P REAL A+ D   + VTG+ RLKLYKGNV ++GR +P SLY +
Sbjct: 305 IGQDYANIIYNGTWFSPMREALDAFVDVTQKPVTGMVRLKLYKGNVTLLGRTSPNSLYNE 364

Query: 361 DLVSFDEAGGYDQKDAEGFIKIQALRLR 388
           +L ++ EA  ++ K AEGFI++  L L+
Sbjct: 365 ELATYTEADTFNHKAAEGFIQLYGLGLK 392


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: 423
Number of extensions: 15
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: 400
Length of database: 401
Length adjustment: 31
Effective length of query: 369
Effective length of database: 370
Effective search space:   136530
Effective search space used:   136530
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_012502227.1 CPAR_RS05030 (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.8790.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.8e-158  513.3   0.0   3.4e-158  513.0   0.0    1.0  1  lcl|NCBI__GCF_000020505.1:WP_012502227.1  CPAR_RS05030 argininosuccinate s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020505.1:WP_012502227.1  CPAR_RS05030 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  513.0   0.0  3.4e-158  3.4e-158       1     391 [.       5     396 ..       5     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 513.0 bits;  conditional E-value: 3.4e-158
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek..gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkd 67 
                                               k+++aysGGlDtsv++k+l++k  gae++avt ++Gq + ++d+ e kal+ Ga  +  +D r+ fv+d
  lcl|NCBI__GCF_000020505.1:WP_012502227.1   5 KIAVAYSGGLDTSVMIKWLKDKyeGAEIVAVTGNLGQ-KMEVDNLEPKALATGAASFHFVDLRKTFVED 72 
                                               799*******************99*************.6****************************** PP

                                 TIGR00032  68 ylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlk 136
                                                + +a++a+a+ye++Y+l+taL+Rp++ak+lv+va  eg+++++hGctgKGnDqvRFe+++ +l+p++k
  lcl|NCBI__GCF_000020505.1:WP_012502227.1  73 CIWKALKAGALYEDVYPLATALGRPILAKALVDVALAEGCTMLTHGCTGKGNDQVRFEVTFASLAPHMK 141
                                               ********************************************************************* PP

                                 TIGR00032 137 viaPvreleli.ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdp 204
                                               v+aP+re+e++ Re+ei ya e+ i+v ++k+++ysiDen++g+siE+g LEdp++ pp d+y+++ +p
  lcl|NCBI__GCF_000020505.1:WP_012502227.1 142 VVAPLREWEFTsREQEITYALEHNIPVSATKKNPYSIDENIWGISIECGVLEDPMVPPPADAYQITTSP 210
                                               **********99*******************************************************99 PP

                                 TIGR00032 205 iektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapa 273
                                               +e++ d+p vv+i+F +G+Pval+g+++e ++li k+ne++  +GvGr+D++E+R++g+KsReiYEapa
  lcl|NCBI__GCF_000020505.1:WP_012502227.1 211 EEAP-DKPTVVDIDFVEGIPVALDGQQMEGLDLIVKLNELGAMNGVGRLDMIENRVVGIKSREIYEAPA 278
                                               9998.**************************************************************** PP

                                 TIGR00032 274 lllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfk 342
                                               +++L+ Ah++Le l+l+k+v ++k+ +++ y+++iY+G wf+p +ealda+++ tq+ vtG+vr+kl+k
  lcl|NCBI__GCF_000020505.1:WP_012502227.1 279 ATILHFAHRELERLTLEKSVFQYKRNIGQDYANIIYNGTWFSPMREALDAFVDVTQKPVTGMVRLKLYK 347
                                               ********************************************************************* PP

                                 TIGR00032 343 GnaivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqikvyre 391
                                               Gn++ +gr+s++slY+eel+++++ ++f++k+a+Gfi+++gl  k+y+e
  lcl|NCBI__GCF_000020505.1:WP_012502227.1 348 GNVTLLGRTSPNSLYNEELATYTEADTFNHKAAEGFIQLYGLGLKTYSE 396
                                               ********************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (401 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: 9.68
//
[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