Alignments for a candidate for astB in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for astB in Caulobacter crescentus NA1000

Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate CCNA_01680 CCNA_01680 succinylarginine dihydrolase

Query= reanno::SB2B:6937151
         (444 letters)



>FitnessBrowser__Caulo:CCNA_01680
          Length = 446

 Score =  416 bits (1068), Expect = e-120
 Identities = 223/445 (50%), Positives = 287/445 (64%), Gaps = 9/445 (2%)

Query: 4   FEANFDGLVGPTHNYAGLSFGNVASQSNAAQVSNPKDAAKQGLKKAKALADMGMVQGMLA 63
           FEAN DGLVGPTH+Y GLS GN+AS  NA +VSNP+ AA +GL K + LAD+G+ Q +L 
Sbjct: 5   FEANCDGLVGPTHSYVGLSPGNLASTRNAGEVSNPRGAALEGLAKMRRLADLGLPQFVLP 64

Query: 64  PQERPDIHTLRRVGFTGSDADVLSQAAKASPVLLQACASASSMWTANAATVSPSADSDDG 123
           P ERP +  LR++GF+G D  VL+ A + +P L  A  SAS MW ANAATV+PSAD+ DG
Sbjct: 65  PHERPAVSLLRQLGFSGPDEIVLTSAWRDAPALAAAACSASPMWAANAATVTPSADAADG 124

Query: 124 KLHFTPANLVDKLHRSIEPVTTGNILKAIFTDERYFAHHQHLPEHPHFGDEGAANHTRLC 183
           ++HFTPANL+  LHRS+E   T   L+ +F DE  FA H  LP  PHF DEGAANH RLC
Sbjct: 125 RVHFTPANLLTNLHRSLEGRQTARSLRRLFADETRFAVHDPLPAQPHFADEGAANHVRLC 184

Query: 184 HDYGQAGVEVFVYGRSVADLSRPAPVKYPARQTLEASQAVARLHQLSDDRTVYMQQNPDV 243
            ++G  GV +FV+GR   +       ++PARQT EA +A+ R H  +  R V+ QQ    
Sbjct: 185 AEHGGPGVNLFVWGR---EAWSHWDGRFPARQTKEAFEAIQRRHGAA--RAVFPQQGKAA 239

Query: 244 IDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEIDKKMHG--NMYFIEVPTAKVSVQD 301
           I+ G FHNDV+ VG +  LF+HE+AF +      E+     G     F+EV  A + + D
Sbjct: 240 IEGGAFHNDVVCVGTRECLFFHERAFEDRATMAREVRAAASGLFEPAFVEVTEADLPMAD 299

Query: 302 AVKSYLFNTQIITL-SDGNMAIIAPTDCQENPAVHAYLNELVTLNTPIKAVHYFDVKQSM 360
            V SYLFN+Q++ +  +  + ++AP + ++NP  +A    L T N PI  V Y DV+QSM
Sbjct: 300 LVASYLFNSQLLVVPGEDRLVLLAPVETRDNPRAYAVAESLATSNGPIGRVEYVDVRQSM 359

Query: 361 QNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADPQLL 420
           +NGGGPACLRLRV + E ELAA NP       L   L  W+ + YRDRLS  DLAD +LL
Sbjct: 360 RNGGGPACLRLRVVLTEAELAAANPAQRFTADLQDALADWITRRYRDRLSPADLADAKLL 419

Query: 421 MESRTALDELTQIMKLG-SVYQFQR 444
            ESR ALDELTQI+ LG   Y FQR
Sbjct: 420 TESREALDELTQILGLGDDFYPFQR 444


Lambda     K      H
   0.318    0.131    0.380 

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: 496
Number of extensions: 23
Number of successful extensions: 5
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: 444
Length of database: 446
Length adjustment: 32
Effective length of query: 412
Effective length of database: 414
Effective search space:   170568
Effective search space used:   170568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate CCNA_01680 CCNA_01680 (succinylarginine dihydrolase)
to HMM TIGR03241 (astB: succinylarginine dihydrolase (EC 3.5.3.23))

# 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.carbon/TIGR03241.hmm
# target sequence database:        /tmp/gapView.3543.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03241  [M=443]
Accession:   TIGR03241
Description: arg_catab_astB: succinylarginine dihydrolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-170  553.9   0.0   1.8e-170  553.7   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01680  CCNA_01680 succinylarginine dihy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01680  CCNA_01680 succinylarginine dihydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.7   0.0  1.8e-170  1.8e-170       1     443 []       4     443 ..       4     443 .. 0.97

  Alignments for each domain:
  == domain 1  score: 553.7 bits;  conditional E-value: 1.8e-170
                             TIGR03241   1 ayevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqerpdiaalrk 73 
                                           a+e+n dGlvG+th y Gls Gn ast+n  +vsnp+ aa  Gl+km+ ladlG+ q vl+p+erp+++ lr+
  lcl|FitnessBrowser__Caulo:CCNA_01680   4 AFEANCDGLVGPTHSYVGLSPGNLASTRNAGEVSNPRGAALEGLAKMRRLADLGLPQFVLPPHERPAVSLLRQ 76 
                                           79*********************************************************************** PP

                             TIGR03241  74 lGfsGsdeevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanlnnkfhrsieaetterv 146
                                           lGfsG de vl+ a r+ap l +a++sas+mw+anaatv+psad+adgrvhft+anl + +hrs+e   t+r 
  lcl|FitnessBrowser__Caulo:CCNA_01680  77 LGFSGPDEIVLTSAWRDAPALAAAACSASPMWAANAATVTPSADAADGRVHFTPANLLTNLHRSLEGRQTARS 149
                                           ************************************************************************* PP

                             TIGR03241 147 lkaifadekkfavhealpavallGdeGaanhtrlgaeydepgvelfvyGraalerepkpkryparqtleasqa 219
                                           l+ +fade++favh+ lpa+ ++ deGaanh rl+ae++ pgv+lfv+Gr+a+++     r+parqt ea +a
  lcl|FitnessBrowser__Caulo:CCNA_01680 150 LRRLFADETRFAVHDPLPAQPHFADEGAANHVRLCAEHGGPGVNLFVWGREAWSH--WDGRFPARQTKEAFEA 220
                                           ****************************************************765..578************* PP

                             TIGR03241 220 varlhqleeekvvyaqqnpdvidqGvfhndviavsnrevlfhhekaflnqsqvldelraklaalgqelvaiev 292
                                           + r+h+   +++v+ qq  ++i+ G fhndv++v+ re lf+he+af +++ +  e+ra  ++l  e   +ev
  lcl|FitnessBrowser__Caulo:CCNA_01680 221 IQRRHGA--ARAVFPQQGKAAIEGGAFHNDVVCVGTRECLFFHERAFEDRATMAREVRAAASGL-FEPAFVEV 290
                                           *****96..689***********************************************99998.566789** PP

                             TIGR03241 293 pdaevsvedavssylfnsqllske.dgkmllvvpeecreneavwayldelvaadgpikevkvfdlresmknGG 364
                                           ++a++ ++d v sylfnsqll    +++++l+ p e+r+n++ +a  ++l++++gpi +v+  d+r+sm+nGG
  lcl|FitnessBrowser__Caulo:CCNA_01680 291 TEADLPMADLVASYLFNSQLLVVPgEDRLVLLAPVETRDNPRAYAVAESLATSNGPIGRVEYVDVRQSMRNGG 363
                                           ********************9987256678899**************************************** PP

                             TIGR03241 365 GpaclrlrvvlndaelaavnpkvllsdalfatlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlG 437
                                           Gpaclrlrvvl++aelaa np+  +++ l ++l +w+ r+yrdrls +dlad +ll+esr+aldeltqil+lG
  lcl|FitnessBrowser__Caulo:CCNA_01680 364 GPACLRLRVVLTEAELAAANPAQRFTADLQDALADWITRRYRDRLSPADLADAKLLTESREALDELTQILGLG 436
                                           ************************************************************************* PP

                             TIGR03241 438 s.vyefq 443
                                              y+fq
  lcl|FitnessBrowser__Caulo:CCNA_01680 437 DdFYPFQ 443
                                           5489998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (446 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.49
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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

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 catabolism of small carbon sources