Alignments for a candidate for argG in Chlorobaculum tepidum TLS

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Chlorobaculum tepidum TLS

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate NP_662005.1 CT1114 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>NCBI__GCF_000006985.1:NP_662005.1
          Length = 401

 Score =  391 bits (1004), Expect = e-113
 Identities = 189/388 (48%), Positives = 268/388 (69%), Gaps = 1/388 (0%)

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

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

Query: 121 DQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLH 180
           DQVRFE+   AL P +KV+AP REW F  R++ IAYA  H IPV  T++ PYS+D N+  
Sbjct: 125 DQVRFEVAFAALAPHMKVVAPLREWEFTSREQEIAYAMEHNIPVSATKKNPYSIDENIWG 184

Query: 181 ISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQ 240
           IS E GVLEDP   PP   +++T  PE APD P  V++EF +G PVA++G+++    L+ 
Sbjct: 185 ISIECGVLEDPMVAPPADAYQITTAPELAPDEPTVVDIEFAQGVPVALDGQQMEGLDLIV 244

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

Query: 301 LSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQ 360
           +   YA L+Y G W++P R+AL A+ D   + VTG+ R+KLYKG++ ++GR +P SLY +
Sbjct: 305 IGQDYANLIYNGTWFSPMRKALDAFVDETQKPVTGMVRIKLYKGSMTLLGRTSPNSLYNE 364

Query: 361 DLVSFDEAGGYDQKDAEGFIKIQALRLR 388
            L ++ EA  +D K AEGFIKI  L L+
Sbjct: 365 ALATYTEADTFDHKSAEGFIKIYGLGLK 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: 420
Number of extensions: 18
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 NP_662005.1 CT1114 (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.30349.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   6.7e-160  518.6   0.0   7.6e-160  518.4   0.0    1.0  1  lcl|NCBI__GCF_000006985.1:NP_662005.1  CT1114 argininosuccinate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000006985.1:NP_662005.1  CT1114 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.4   0.0  7.6e-160  7.6e-160       1     392 [.       5     397 ..       5     399 .. 0.99

  Alignments for each domain:
  == domain 1  score: 518.4 bits;  conditional E-value: 7.6e-160
                              TIGR00032   1 kvvlaysGGlDtsvalklleek..gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylf 70 
                                            k+++aysGGlDtsv++k+l++k  gae++avt ++Gq + ++d+ e+ka++ Ga+ +  +D r+ fv++y+ 
  lcl|NCBI__GCF_000006985.1:NP_662005.1   5 KIAVAYSGGLDTSVMIKWLKDKyeGAEIVAVTGNLGQ-KMEVDNLEQKAIATGAKSFHFVDLRKTFVEEYIW 75 
                                            799*******************99*************.6********************************* PP

                              TIGR00032  71 aaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvr 142
                                            +a++a+a+ye++Y+l+taL+Rpl+ak+lv+va  eg+++++hGctgKGnDqvRFe+ + +l+p++kv+aP+r
  lcl|NCBI__GCF_000006985.1:NP_662005.1  76 KALKAGALYEDVYPLATALGRPLLAKALVDVALAEGCTMLTHGCTGKGNDQVRFEVAFAALAPHMKVVAPLR 147
                                            ************************************************************************ PP

                              TIGR00032 143 eleli.ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepe 213
                                            e+e++ Re+ei+ya e+ i+v ++k+++ysiDen++g+siE+g LEdp+++pp d+y+++  p+ ++ dep 
  lcl|NCBI__GCF_000006985.1:NP_662005.1 148 EWEFTsREQEIAYAMEHNIPVSATKKNPYSIDENIWGISIECGVLEDPMVAPPADAYQITTAPELAP-DEPT 218
                                            ****99*******************************************************777777.**** PP

                              TIGR00032 214 vveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLe 285
                                            vv+ieF +GvPval+g+++e ++li ++ne++  +GvGr+D++E+R++g+KsReiYEapa+++L+ Ah++Le
  lcl|NCBI__GCF_000006985.1:NP_662005.1 219 VVDIEFAQGVPVALDGQQMEGLDLIVRLNELGAMNGVGRLDMIENRVVGIKSREIYEAPAATILHFAHRELE 290
                                            ************************************************************************ PP

                              TIGR00032 286 tlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslY 357
                                             l+l+k+v ++k+ +++ y++liY+G wf+p ++alda++++tq+ vtG+vr+kl+kG+++ +gr+s++slY
  lcl|NCBI__GCF_000006985.1:NP_662005.1 291 RLTLEKSVFQYKRNIGQDYANLIYNGTWFSPMRKALDAFVDETQKPVTGMVRIKLYKGSMTLLGRTSPNSLY 362
                                            ************************************************************************ PP

                              TIGR00032 358 deelvsfekdkefdqkdaiGfikirglqikvyrek 392
                                            +e l+++++ ++fd+k a+Gfiki+gl  k+++e+
  lcl|NCBI__GCF_000006985.1:NP_662005.1 363 NEALATYTEADTFDHKSAEGFIKIYGLGLKTFHEV 397
                                            ***************************99998876 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.38
//
[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