GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Sinorhizobium fredii NGR234

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_012706739.1 NGR_RS12140 ornithine carbamoyltransferase

Query= BRENDA::Q98BB6
         (303 letters)



>NCBI__GCF_000018545.1:WP_012706739.1
          Length = 305

 Score =  472 bits (1214), Expect = e-138
 Identities = 228/302 (75%), Positives = 257/302 (85%)

Query: 2   SVRHFTDLSTVSEGDLRFMLDDAVVRKARLKAGERTRPLEGKVLAMIFDKPSTRTRVSFD 61
           + RHF DLS ++  DLR ++DDA VRK   KAG   +PL GK+LAMIF+KPSTRTRVSFD
Sbjct: 3   ATRHFLDLSAMTGADLRTIIDDARVRKTATKAGTAEKPLAGKMLAMIFEKPSTRTRVSFD 62

Query: 62  VGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENATVP 121
           VGMRQLGGET+ L+GTEMQLGR+ETI DTAKVLSRYVDAIMIRTT H RLLEL E+ATVP
Sbjct: 63  VGMRQLGGETLFLSGTEMQLGRAETIGDTAKVLSRYVDAIMIRTTDHRRLLELAEHATVP 122

Query: 122 VINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNLNVA 181
           VINGLTDDTHPCQ+MADIMTFEEHRGPV GKTIAWTGDGNNVLHSL+E SARF + +N+A
Sbjct: 123 VINGLTDDTHPCQIMADIMTFEEHRGPVQGKTIAWTGDGNNVLHSLIEGSARFGYRMNMA 182

Query: 182 VPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGHNVFSP 241
           VP GSEP  K ++W++ +GG++      E+AV  A CVVTD WVSM QEHRARGHNVF P
Sbjct: 183 VPLGSEPQDKFLNWARNNGGEILLCHEAEQAVAGAHCVVTDTWVSMNQEHRARGHNVFQP 242

Query: 242 YQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAVLAWCL 301
           YQVNA LM HA P+A+FMHCLPAHRGEEVTDEVIDGP SVVFD AENRLHAQK++LAWCL
Sbjct: 243 YQVNAALMKHAVPEAVFMHCLPAHRGEEVTDEVIDGPQSVVFDAAENRLHAQKSILAWCL 302

Query: 302 GA 303
           GA
Sbjct: 303 GA 304


Lambda     K      H
   0.320    0.133    0.400 

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: 411
Number of extensions: 16
Number of successful extensions: 1
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: 303
Length of database: 305
Length adjustment: 27
Effective length of query: 276
Effective length of database: 278
Effective search space:    76728
Effective search space used:    76728
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_012706739.1 NGR_RS12140 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

# 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/TIGR00658.hmm
# target sequence database:        /tmp/gapView.3413025.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00658  [M=304]
Accession:   TIGR00658
Description: orni_carb_tr: ornithine carbamoyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-119  383.3   0.0   4.5e-119  383.1   0.0    1.0  1  NCBI__GCF_000018545.1:WP_012706739.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_012706739.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.1   0.0  4.5e-119  4.5e-119       1     303 [.       5     302 ..       5     303 .. 0.98

  Alignments for each domain:
  == domain 1  score: 383.1 bits;  conditional E-value: 4.5e-119
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 
                                           rh+l+l  ++ ++l+++++ a+  k+++k+g+ ek l gk la+iFek+stRtRvsf+v++ +lG+++l+l+ 
  NCBI__GCF_000018545.1:WP_012706739.1   5 RHFLDLSAMTGADLRTIIDDARVRKTATKAGTAEKPLAGKMLAMIFEKPSTRTRVSFDVGMRQLGGETLFLSG 77 
                                           8************************************************************************ PP

                             TIGR00658  74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgkl 146
                                            e+qlgr e+i Dta+vlsryvdai++R+++h+ + ela++a+vPvingLtd +hPcqi+aD++t +e+ g +
  NCBI__GCF_000018545.1:WP_012706739.1  78 TEMQLGRAETIGDTAKVLSRYVDAIMIRTTDHRRLLELAEHATVPVINGLTDDTHPCQIMADIMTFEEHRGPV 150
                                           ************************************************************************* PP

                             TIGR00658 147 kevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadv 219
                                           ++ ++++ GD+nnv +sl+ ++a +G  +++a P g ep+ + +++a+    +ngg++ l ++ ++av++a+ 
  NCBI__GCF_000018545.1:WP_012706739.1 151 QGKTIAWTGDGNNVLHSLIEGSARFGYRMNMAVPLGSEPQDKFLNWAR----NNGGEILLCHEAEQAVAGAHC 219
                                           *********************************************995....6******************** PP

                             TIGR00658 220 iytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRl 292
                                           ++tD+wvsm +e+++    ++++pyqvn  l+++a pe++f+hCLPa+rGeevtdev++g++s+vfd aenRl
  NCBI__GCF_000018545.1:WP_012706739.1 220 VVTDTWVSMNQEHRA-RGHNVFQPYQVNAALMKHAVPEAVFMHCLPAHRGEEVTDEVIDGPQSVVFDAAENRL 291
                                           **********99887.5679***************************************************** PP

                             TIGR00658 293 haqkavlkall 303
                                           haqk++l+++l
  NCBI__GCF_000018545.1:WP_012706739.1 292 HAQKSILAWCL 302
                                           *******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (305 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 22.27
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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:

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:

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:

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