Alignments for a candidate for astB in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for astB in Marinobacter adhaerens HP15

Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate GFF3095 HP15_3038 N-succinylarginine dihydrolase

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



>FitnessBrowser__Marino:GFF3095
          Length = 446

 Score =  540 bits (1391), Expect = e-158
 Identities = 280/445 (62%), Positives = 326/445 (73%), Gaps = 3/445 (0%)

Query: 1   MKH-FEANFDGLVGPTHNYAGLSFGNVASQSNAAQVSNPKDAAKQGLKKAKALADMGMVQ 59
           +KH  EANFDGLVGPTHNYAGLS+GNVAS+SN + VSNPK+AA QGL K K LAD G VQ
Sbjct: 2   VKHAVEANFDGLVGPTHNYAGLSWGNVASKSNVSSVSNPKEAALQGLAKMKRLADRGYVQ 61

Query: 60  GMLAPQERPDIHTLRRVGFTGSDADVLSQAAKASPVLLQACASASSMWTANAATVSPSAD 119
           G+L P ERP I TLR +GF G DA VL QAAK+SP +L A +SAS MWTANAATVSPSAD
Sbjct: 62  GVLPPHERPHIPTLRALGFEGPDARVLEQAAKSSPSILAAVSSASPMWTANAATVSPSAD 121

Query: 120 SDDGKLHFTPANLVDKLHRSIEPVTTGNILKAIFTDERYFAHHQHLPEHPHFGDEGAANH 179
           + D ++HFTPANL  K HRSIE   TG  LK+IF DE YFAHH  LP   HFGDEGAANH
Sbjct: 122 TSDHRVHFTPANLSAKFHRSIEHAVTGRALKSIFADESYFAHHPALPSVSHFGDEGAANH 181

Query: 180 TRLCHDYGQAGVEVFVYGRSVADLSRPAPVKYPARQTLEASQAVARLHQLSDDRTVYMQQ 239
           TRLC  YG+ GVE+FVYG+   +   PAP KYPARQTLEASQAVARLH L D   V+ QQ
Sbjct: 182 TRLCAGYGEPGVELFVYGQMAFNEQAPAPKKYPARQTLEASQAVARLHGLRDQNAVFAQQ 241

Query: 240 NPDVIDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEIDKKMHG-NMYFIEVPTAKVS 298
           NPD ID GVFHNDVIAVGN N LFYHE AFL     LA+I +++ G  +  + V +A V 
Sbjct: 242 NPDAIDGGVFHNDVIAVGNGNTLFYHEMAFLNEAQVLADIRERLTGAELEAVRVSSADVP 301

Query: 299 VQDAVKSYLFNTQIITLSDGNMAIIAPTDCQENPAVHAYLNELVTLNTPIKAVHYFDVKQ 358
           ++DAV SYLFN+Q++   DG M +  P +C+E  +V  YL+ LV    PI AV  FDVKQ
Sbjct: 302 LEDAVASYLFNSQLLNTPDG-MLLAVPGECREVASVSRYLDGLVKSGGPITAVEVFDVKQ 360

Query: 359 SMQNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADPQ 418
           SM+NGGGPACLRLRV +N+ EL A+N  V++ D L+ RL  WV+ HYRD LS  +L DP 
Sbjct: 361 SMRNGGGPACLRLRVVLNDDELKAINRGVLLTDELYERLTTWVEAHYRDELSQNELGDPM 420

Query: 419 LLMESRTALDELTQIMKLGSVYQFQ 443
           LL E R ALDELT IM LGS+Y FQ
Sbjct: 421 LLEEVRKALDELTGIMGLGSIYDFQ 445


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: 552
Number of extensions: 18
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: 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 GFF3095 HP15_3038 (N-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.17383.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.6e-226  736.2   0.0   8.6e-226  736.0   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3095  HP15_3038 N-succinylarginine dih


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3095  HP15_3038 N-succinylarginine dihydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  736.0   0.0  8.6e-226  8.6e-226       1     443 []       5     445 ..       5     445 .. 0.99

  Alignments for each domain:
  == domain 1  score: 736.0 bits;  conditional E-value: 8.6e-226
                           TIGR03241   1 ayevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqerpdiaalrklG 75 
                                         a e+nfdGlvG+thnyaGls+Gn+as+sn +svsnpk+aa qGl+kmk lad G+ qgvl+p+erp+i++lr lG
  lcl|FitnessBrowser__Marino:GFF3095   5 AVEANFDGLVGPTHNYAGLSWGNVASKSNVSSVSNPKEAALQGLAKMKRLADRGYVQGVLPPHERPHIPTLRALG 79 
                                         579************************************************************************ PP

                           TIGR03241  76 fsGsdeevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanlnnkfhrsieaettervlkai 150
                                         f G d+ vle+aa+++p++l+avssas+mwtanaatvspsadt+d rvhft+anl++kfhrsie+++t r+lk+i
  lcl|FitnessBrowser__Marino:GFF3095  80 FEGPDARVLEQAAKSSPSILAAVSSASPMWTANAATVSPSADTSDHRVHFTPANLSAKFHRSIEHAVTGRALKSI 154
                                         *************************************************************************** PP

                           TIGR03241 151 fadekkfavhealpavallGdeGaanhtrlgaeydepgvelfvyGraal.erepkpkryparqtleasqavarlh 224
                                         fade++fa+h alp+v+++GdeGaanhtrl+a y+epgvelfvyG+ a+ e++p+pk+yparqtleasqavarlh
  lcl|FitnessBrowser__Marino:GFF3095 155 FADESYFAHHPALPSVSHFGDEGAANHTRLCAGYGEPGVELFVYGQMAFnEQAPAPKKYPARQTLEASQAVARLH 229
                                         *************************************************8899********************** PP

                           TIGR03241 225 qleeekvvyaqqnpdvidqGvfhndviavsnrevlfhhekaflnqsqvldelraklaalgqelvaievpdaevsv 299
                                         +l+++++v+aqqnpd+id Gvfhndviav+n ++lf+he afln++qvl+++r++l++   el+a++v++a+v +
  lcl|FitnessBrowser__Marino:GFF3095 230 GLRDQNAVFAQQNPDAIDGGVFHNDVIAVGNGNTLFYHEMAFLNEAQVLADIRERLTGA--ELEAVRVSSADVPL 302
                                         ********************************************************987..9************* PP

                           TIGR03241 300 edavssylfnsqllskedgkmllvvpeecreneavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvv 374
                                         edav sylfnsqll+  dg mll vp ecre ++v +yld lv+++gpi+ v+vfd+++sm+nGGGpaclrlrvv
  lcl|FitnessBrowser__Marino:GFF3095 303 EDAVASYLFNSQLLNTPDG-MLLAVPGECREVASVSRYLDGLVKSGGPITAVEVFDVKQSMRNGGGPACLRLRVV 376
                                         ***************9998.999**************************************************** PP

                           TIGR03241 375 lndaelaavnpkvllsdalfatlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsvyefq 443
                                         lnd+el+a+n+ vll+d+l+++l++wv+ hyrd+ls+++l dp ll+e+r+aldelt i++lGs+y+fq
  lcl|FitnessBrowser__Marino:GFF3095 377 LNDDELKAINRGVLLTDELYERLTTWVEAHYRDELSQNELGDPMLLEEVRKALDELTGIMGLGSIYDFQ 445
                                         ********************************************************************9 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.23
//
[ok]

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