Alignments for a candidate for arcB in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Sphingomonas koreensis DSMZ 15582

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate Ga0059261_3206 Ga0059261_3206 ornithine carbamoyltransferase

Query= BRENDA::Q98BB6
         (303 letters)



>FitnessBrowser__Korea:Ga0059261_3206
          Length = 307

 Score =  308 bits (789), Expect = 1e-88
 Identities = 162/308 (52%), Positives = 203/308 (65%), Gaps = 10/308 (3%)

Query: 1   MSVRHFTDLSTVSEGDLRFMLDDAVVRKARLKAGE------RTRPLEGKVLAMIFDKPST 54
           M+ R+F  LS      +  ML DA+ RK R +AG+         PL G+ LAM+F+K ST
Sbjct: 1   MTYRNFLSLSDAGADGIAAMLADAIDRK-RARAGQPKGAVDADAPLAGRTLAMVFEKNST 59

Query: 55  RTRVSFDVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLEL 114
           RTRVSF++ +RQLGG  ++L     QLGR ET+ADTA+VLS Y DAIM+RT  H +LLE+
Sbjct: 60  RTRVSFEMAIRQLGGSAVVLDAATSQLGRGETVADTARVLSGYCDAIMVRTDDHAKLLEM 119

Query: 115 TENATVPVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARF 174
            + ATVPVINGLTDD+HPCQ+MAD+ T  E    + G  +AW GDGNNVL S++EA+   
Sbjct: 120 AQYATVPVINGLTDDSHPCQIMADLQTILESGKALPGLKVAWLGDGNNVLASIVEAAGLM 179

Query: 175 RFNLNVAVPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRAR 234
            F++  A P+     ++ +   K   G+      P EAV  AD VVTD W+SMGQ H   
Sbjct: 180 HFDVVAACPQSFALPEEAMALGK---GRARTVNDPVEAVAGADVVVTDTWISMGQAHADV 236

Query: 235 GHNVFSPYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQK 294
                +PYQV   LMA A PDA F+HCLPAHRGEEVTD VIDGP S+++ EAENRLHAQK
Sbjct: 237 KLAALAPYQVTEALMAQASPDAKFLHCLPAHRGEEVTDAVIDGPQSLIWPEAENRLHAQK 296

Query: 295 AVLAWCLG 302
           AVL WC G
Sbjct: 297 AVLRWCFG 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: 321
Number of extensions: 14
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: 303
Length of database: 307
Length adjustment: 27
Effective length of query: 276
Effective length of database: 280
Effective search space:    77280
Effective search space used:    77280
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 Ga0059261_3206 Ga0059261_3206 (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.32493.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-107  344.8   0.0   2.4e-107  344.6   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3206  Ga0059261_3206 ornithine carbamo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3206  Ga0059261_3206 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.6   0.0  2.4e-107  2.4e-107       1     303 [.       4     303 ..       4     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 344.6 bits;  conditional E-value: 2.4e-107
                                 TIGR00658   1 rhllslldlseeelkellelakklkkekkkgke.....ekklkgktlaliFekrstRtRvsfevaayel 64 
                                               r++lsl d   + +  +l  a + k+++  + +     ++ l g+tla++Fek+stRtRvsfe+a+ +l
  lcl|FitnessBrowser__Korea:Ga0059261_3206   4 RNFLSLSDAGADGIAAMLADAIDRKRARAGQPKgavdaDAPLAGRTLAMVFEKNSTRTRVSFEMAIRQL 72 
                                               789*******************9999887655456677899**************************** PP

                                 TIGR00658  65 GaqvlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqil 133
                                               G+ +++l++  +qlgr+e+++Dtarvls y dai+vR+ +h ++ e+a+ya+vPvingLtd +hPcqi+
  lcl|FitnessBrowser__Korea:Ga0059261_3206  73 GGSAVVLDAATSQLGRGETVADTARVLSGYCDAIMVRTDDHAKLLEMAQYATVPVINGLTDDSHPCQIM 141
                                               ********************************************************************* PP

                                 TIGR00658 134 aDlltikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakengg 202
                                               aDl+ti e  ++l ++k++++GD+nnv  s++ aa ++ +dvv a+P+ +   +e +           g
  lcl|FitnessBrowser__Korea:Ga0059261_3206 142 ADLQTILESGKALPGLKVAWLGDGNNVLASIVEAAGLMHFDVVAACPQSFALPEEAMAL-------GKG 203
                                               ************************************************99766554433.......348 PP

                                 TIGR00658 203 kleltedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGee 271
                                               + + ++dp++av++adv++tD+w+smG+ ++ + +l++l pyqv+e l++ a p++kflhCLPa+rGee
  lcl|FitnessBrowser__Korea:Ga0059261_3206 204 RARTVNDPVEAVAGADVVVTDTWISMGQAHA-DVKLAALAPYQVTEALMAQASPDAKFLHCLPAHRGEE 271
                                               9999***********************9765.59*********************************** PP

                                 TIGR00658 272 vtdevlegeasivfdeaenRlhaqkavlkall 303
                                               vtd v++g++s+++ eaenRlhaqkavl +++
  lcl|FitnessBrowser__Korea:Ga0059261_3206 272 VTDAVIDGPQSLIWPEAENRLHAQKAVLRWCF 303
                                               ****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (307 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: 00:00:00.02
# Mc/sec: 4.01
//
[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