Aligments for a candidate for argG in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Aligments for a candidate for argG in Caulobacter crescentus NA1000

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate CCNA_00128 CCNA_00128 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__Caulo:CCNA_00128
          Length = 408

 Score =  487 bits (1253), Expect = e-142
 Identities = 248/401 (61%), Positives = 302/401 (75%), Gaps = 5/401 (1%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGAS--KAIAL 59
           K+VLAYSGGLDTSIILKWL+  Y AEVI FTAD+GQGEE+E AR KAL  G         
Sbjct: 8   KVVLAYSGGLDTSIILKWLQTEYGAEVITFTADLGQGEEIEPARAKALAAGVKPENIFIE 67

Query: 60  DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119
           D++EEFVRD+VFPM RA  VYEG YLLGTSIARPLIAK  + IA + GA+A++HGATGKG
Sbjct: 68  DVREEFVRDYVFPMFRANTVYEGQYLLGTSIARPLIAKKQIEIARKMGADAVSHGATGKG 127

Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQ--EKPYSMDAN 177
           NDQVRFEL  Y L+PDI VIAPWREW F+ R+ ++ +AE H I +   +  E P+S+DAN
Sbjct: 128 NDQVRFELGYYGLEPDITVIAPWREWDFKSREALLDFAEKHQIQITKDKRGEAPFSVDAN 187

Query: 178 LLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAA 237
           LLH S EG VLEDP  E P+ +   T  PE+APDAP  + ++F +GDPVA++G  +SPA 
Sbjct: 188 LLHSSSEGKVLEDPAVEAPEFVHMRTIAPEDAPDAPTIITIDFEKGDPVAIDGVAMSPAT 247

Query: 238 LLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQ 297
           LL +LNE+G  +GVGR+D+VENRFVGMKSRGVYETPGGTIL  A R +ES+TLDR  +H 
Sbjct: 248 LLTKLNELGRDNGVGRLDLVENRFVGMKSRGVYETPGGTILLAAHRGIESITLDRGAMHL 307

Query: 298 RDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSL 357
           +D L PKYA LVY GFW++PERE LQA  D+    VTG  R+KLYKGNV V+GR++P SL
Sbjct: 308 KDELMPKYASLVYNGFWFSPEREMLQAAIDYSQDKVTGRVRVKLYKGNVTVIGRESPYSL 367

Query: 358 YRQDLVSFDEAG-GYDQKDAEGFIKIQALRLRVRALVEREG 397
           Y QDLV+F+E    YD +DA GFIK+ ALRLRV A  ++ G
Sbjct: 368 YDQDLVTFEEGKVAYDHRDAGGFIKLNALRLRVLAKRDKRG 408


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: 516
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 CCNA_00128 CCNA_00128 (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.26731.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-146  473.6   0.0   3.6e-146  473.4   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00128  CCNA_00128 argininosuccinate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00128  CCNA_00128 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.4   0.0  3.6e-146  3.6e-146       1     391 [.       8     403 ..       8     406 .. 0.97

  Alignments for each domain:
  == domain 1  score: 473.4 bits;  conditional E-value: 3.6e-146
                             TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGae..kayviDareefvkdylf 70 
                                           kvvlaysGGlDts++lk+l+ + gaevi++t+d+Gq+ e+++ ++ kal+ G++  +  + D reefv+dy+f
  lcl|FitnessBrowser__Caulo:CCNA_00128   8 KVVLAYSGGLDTSIILKWLQTEyGAEVITFTADLGQG-EEIEPARAKALAAGVKpeNIFIEDVREEFVRDYVF 79 
                                           8*********************9*************9.9*************863266677************ PP

                             TIGR00032  71 aaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvre 143
                                           +  +an+vyeg+Yll+t++aRpliakk++e+a+k ga+av+hG+tgKGnDqvRFel  + l+pd+ viaP+re
  lcl|FitnessBrowser__Caulo:CCNA_00128  80 PMFRANTVYEGQYLLGTSIARPLIAKKQIEIARKMGADAVSHGATGKGNDQVRFELGYYGLEPDITVIAPWRE 152
                                           ************************************************************************* PP

                             TIGR00032 144 leli.ReeeieyaaekGievpvek..ekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepe 213
                                           +++  Re ++++a+++ i++  +k  e ++s+D nll+ s E++ LEdp +e pe +++ +  p++++ d p 
  lcl|FitnessBrowser__Caulo:CCNA_00128 153 WDFKsREALLDFAEKHQIQITKDKrgEAPFSVDANLLHSSSEGKVLEDPAVEAPEFVHMRTIAPEDAP-DAPT 224
                                           ***88**************998875579*********************************9787777.**** PP

                             TIGR00032 214 vveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLet 286
                                           +++i+FekG Pva++g+ ++p +l+ k+ne+++ +GvGr+D vE+R +g+KsR++YE+p+ ++L+ Ah+ +e+
  lcl|FitnessBrowser__Caulo:CCNA_00128 225 IITIDFEKGDPVAIDGVAMSPATLLTKLNELGRDNGVGRLDLVENRFVGMKSRGVYETPGGTILLAAHRGIES 297
                                           ************************************************************************* PP

                             TIGR00032 287 lvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYde 359
                                            +l++  +++k+    ky+ l+Y+G+wf+p++e+l+a+i+ +q++vtG vrvkl+kGn++vigr+s+yslYd+
  lcl|FitnessBrowser__Caulo:CCNA_00128 298 ITLDRGAMHLKDELMPKYASLVYNGFWFSPEREMLQAAIDYSQDKVTGRVRVKLYKGNVTVIGRESPYSLYDQ 370
                                           ************************************************************************* PP

                             TIGR00032 360 elvsfek.dkefdqkdaiGfikirglqikvyre 391
                                           +lv+fe+ + ++d++da Gfik+++l+ +v ++
  lcl|FitnessBrowser__Caulo:CCNA_00128 371 DLVTFEEgKVAYDHRDAGGFIKLNALRLRVLAK 403
                                           ******98889***************9988765 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: 00:00:00.01
# Mc/sec: 10.39
//
[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