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, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate SMa0695 SMa0695 ornithine carbamoyltransferase

Query= SwissProt::P08308
         (336 letters)



>FitnessBrowser__Smeli:SMa0695
          Length = 334

 Score =  488 bits (1257), Expect = e-143
 Identities = 230/335 (68%), Positives = 284/335 (84%), Gaps = 1/335 (0%)

Query: 1   MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60
           M+FN+ NR+LL++  ++ RE RYL+DL+RDLKRAKY  TEQ+HLK K I LIFEKTSTRT
Sbjct: 1   MSFNLRNRSLLTVQDYTPREFRYLVDLARDLKRAKYARTEQEHLKGKEICLIFEKTSTRT 60

Query: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120
           RCAFEVA  DQGANVTY+DP  SQIGHKES KDTARVLGRMYDAIEYRG  Q  VE LAK
Sbjct: 61  RCAFEVACSDQGANVTYLDPAGSQIGHKESFKDTARVLGRMYDAIEYRGASQAGVETLAK 120

Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180
           +AGVPV+NGLTDEYHPTQM+ADV+TMREHSDKP+ +I YAY+GD R+NMG+SLL++G  +
Sbjct: 121 YAGVPVYNGLTDEYHPTQMIADVMTMREHSDKPISEIKYAYIGDTRSNMGHSLLIVGCLM 180

Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240
           GMDVRI  P++LWP +E+    K+   +SGA+L +T++P+EAV+GVDF+HTDVWVSMGEP
Sbjct: 181 GMDVRICGPRSLWPSEEYQTIAKRLKAQSGARLMITDNPREAVEGVDFIHTDVWVSMGEP 240

Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300
            E W ERI+ L PYQVN E+M A+GNP+ KFMHCLPA+H++ET +GKQI++ Y  +++G+
Sbjct: 241 KEVWKERIQLLTPYQVNAELMAASGNPQTKFMHCLPAYHDTETTIGKQISDDY-GMSDGL 299

Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLAD 335
           EVT++VFES  NIAFEQAENRMHTIKA+LV+TL D
Sbjct: 300 EVTDEVFESQANIAFEQAENRMHTIKALLVATLGD 334


Lambda     K      H
   0.318    0.133    0.387 

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: 412
Number of extensions: 10
Number of successful extensions: 2
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: 336
Length of database: 334
Length adjustment: 28
Effective length of query: 308
Effective length of database: 306
Effective search space:    94248
Effective search space used:    94248
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: 49 (23.5 bits)

Align candidate SMa0695 SMa0695 (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.6276.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     1e-129  418.1   0.0   1.1e-129  417.9   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMa0695  SMa0695 ornithine carbamoyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMa0695  SMa0695 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.9   0.0  1.1e-129  1.1e-129       1     303 [.       8     332 ..       8     333 .. 0.99

  Alignments for each domain:
  == domain 1  score: 417.9 bits;  conditional E-value: 1.1e-129
                          TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeel 76 
                                        r+ll+++d++++e+++l++la++lk++k++ +e+++lkgk++ liFek+stRtR++feva  ++Ga+v+yl++  +
  lcl|FitnessBrowser__Smeli:SMa0695   8 RSLLTVQDYTPREFRYLVDLARDLKRAKYARTEQEHLKGKEICLIFEKTSTRTRCAFEVACSDQGANVTYLDPAGS 83 
                                        789************************************************************************* PP

                          TIGR00658  77 qlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg.klkevkl 151
                                        q+g+kes+kDtarvl+r++dai +R+ ++  ve+lakya+vPv+ngLtd+ hP+q++aD++t++e+ +  ++e+k+
  lcl|FitnessBrowser__Smeli:SMa0695  84 QIGHKESFKDTARVLGRMYDAIEYRGASQAGVETLAKYAGVPVYNGLTDEYHPTQMIADVMTMREHSDkPISEIKY 159
                                        ********************************************************************99****** PP

                          TIGR00658 152 vyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwv 226
                                        +y+GD+  n+++sll+ + ++G+dv++++P+ l+p++e+ + ak++ +++g++l +t++p +av+++d+i+tDvwv
  lcl|FitnessBrowser__Smeli:SMa0695 160 AYIGDTrSNMGHSLLIVGCLMGMDVRICGPRSLWPSEEYQTIAKRLKAQSGARLMITDNPREAVEGVDFIHTDVWV 235
                                        ******9********************************************************************* PP

                          TIGR00658 227 smGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr..................Geevtdevlegeas 282
                                        smGe +e ++er++ll pyqvn el++ + +p++kf+hCLPa +                  G evtdev+e++a+
  lcl|FitnessBrowser__Smeli:SMa0695 236 SMGEpKEVWKERIQLLTPYQVNAELMAASgNPQTKFMHCLPAYHdtettigkqisddygmsdGLEVTDEVFESQAN 311
                                        ****9999********************99********************************************** PP

                          TIGR00658 283 ivfdeaenRlhaqkavlkall 303
                                        i f++aenR+h++ka+l+a+l
  lcl|FitnessBrowser__Smeli:SMa0695 312 IAFEQAENRMHTIKALLVATL 332
                                        *****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (334 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.23
//
[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