Alignments for a candidate for arcB in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Sinorhizobium meliloti 1021

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate SMc02137 SMc02137 ornithine carbamoyltransferase

Query= BRENDA::Q98BB6
         (303 letters)



>FitnessBrowser__Smeli:SMc02137
          Length = 303

 Score =  470 bits (1209), Expect = e-137
 Identities = 225/300 (75%), Positives = 257/300 (85%)

Query: 4   RHFTDLSTVSEGDLRFMLDDAVVRKARLKAGERTRPLEGKVLAMIFDKPSTRTRVSFDVG 63
           RHF DLS ++  DLR ++DDA VRK+  KAG   +PL GK+LAMIF+KPSTRTRVSFDVG
Sbjct: 3   RHFLDLSAMTATDLRTIIDDARVRKSATKAGTAEKPLAGKMLAMIFEKPSTRTRVSFDVG 62

Query: 64  MRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENATVPVI 123
           MRQLGGET+ L+GTEMQLGR+ETI DTAKVLSRYVDAIMIRTT H RLLE+ E+ATVPVI
Sbjct: 63  MRQLGGETLFLSGTEMQLGRAETIGDTAKVLSRYVDAIMIRTTDHRRLLEMAEHATVPVI 122

Query: 124 NGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNLNVAVP 183
           NGLTDDTHPCQ+MADI+TFEEHRGPV GKTIAWTGDGNNVLHSL+E SARF + +N+AVP
Sbjct: 123 NGLTDDTHPCQIMADILTFEEHRGPVKGKTIAWTGDGNNVLHSLIEGSARFGYRMNMAVP 182

Query: 184 EGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGHNVFSPYQ 243
            GSEP  K ++W++ +G ++  +   E+AV  A CVVTD W+SM QEHRARGHNVF PYQ
Sbjct: 183 LGSEPHDKFLNWARNNGAEVLLSHEAEQAVAGAHCVVTDTWISMNQEHRARGHNVFQPYQ 242

Query: 244 VNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAVLAWCLGA 303
           VN  LM HA PDALFMHCLPAHRGEEVTDEVIDGP SVVFDEAENRLHAQK++LAWC+GA
Sbjct: 243 VNGALMKHAAPDALFMHCLPAHRGEEVTDEVIDGPQSVVFDEAENRLHAQKSILAWCMGA 302


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: 420
Number of extensions: 19
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: 303
Length adjustment: 27
Effective length of query: 276
Effective length of database: 276
Effective search space:    76176
Effective search space used:    76176
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 SMc02137 SMc02137 (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.32603.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     3e-119  383.7   0.0   3.3e-119  383.5   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc02137  SMc02137 ornithine carbamoyltran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02137  SMc02137 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.5   0.0  3.3e-119  3.3e-119       1     303 [.       3     300 ..       3     301 .. 0.98

  Alignments for each domain:
  == domain 1  score: 383.5 bits;  conditional E-value: 3.3e-119
                           TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkee 75 
                                         rh+l+l  ++  +l+++++ a+  k+++k+g+ ek l gk la+iFek+stRtRvsf+v++ +lG+++l+l+  e
  lcl|FitnessBrowser__Smeli:SMc02137   3 RHFLDLSAMTATDLRTIIDDARVRKSATKAGTAEKPLAGKMLAMIFEKPSTRTRVSFDVGMRQLGGETLFLSGTE 77 
                                         8************************************************************************** PP

                           TIGR00658  76 lqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevk 150
                                         +qlgr e+i Dta+vlsryvdai++R+++h+ + e+a++a+vPvingLtd +hPcqi+aD+lt +e+ g +k+ +
  lcl|FitnessBrowser__Smeli:SMc02137  78 MQLGRAETIGDTAKVLSRYVDAIMIRTTDHRRLLEMAEHATVPVINGLTDDTHPCQIMADILTFEEHRGPVKGKT 152
                                         *************************************************************************** PP

                           TIGR00658 151 lvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvw 225
                                         +++ GD+nnv +sl+ ++a +G  +++a P g ep+ + +++a+    +ng+++ l ++ ++av++a+ ++tD+w
  lcl|FitnessBrowser__Smeli:SMc02137 153 IAWTGDGNNVLHSLIEGSARFGYRMNMAVPLGSEPHDKFLNWAR----NNGAEVLLSHEAEQAVAGAHCVVTDTW 223
                                         *****************************************995....6************************** PP

                           TIGR00658 226 vsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlk 300
                                         +sm +e+++    ++++pyqvn  l+++a p++ f+hCLPa+rGeevtdev++g++s+vfdeaenRlhaqk++l+
  lcl|FitnessBrowser__Smeli:SMc02137 224 ISMNQEHRA-RGHNVFQPYQVNGALMKHAAPDALFMHCLPAHRGEEVTDEVIDGPQSVVFDEAENRLHAQKSILA 297
                                         ****99887.5679************************************************************9 PP

                           TIGR00658 301 all 303
                                         +++
  lcl|FitnessBrowser__Smeli:SMc02137 298 WCM 300
                                         987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (303 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: 7.10
//
[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