GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcC in Pseudomonas fluorescens FW300-N2C3

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate AO356_05280 AO356_05280 carbamate kinase

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05280
          Length = 309

 Score =  512 bits (1318), Expect = e-150
 Identities = 254/310 (81%), Positives = 284/310 (91%), Gaps = 1/310 (0%)

Query: 1   MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60
           MRIVVALGGNALLRRGEP+TA NQR N+R A EQIAK+ PGN+LVIAHGNGPQVGLL+LQ
Sbjct: 1   MRIVVALGGNALLRRGEPLTAANQRSNIRTATEQIAKIHPGNQLVIAHGNGPQVGLLSLQ 60

Query: 61  GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120
            AAY  V+PYPLDVLGAETEGMIGY+IEQE+GNLL FEVPFAT+LTQVEVDG DPAFQNP
Sbjct: 61  AAAYTAVTPYPLDVLGAETEGMIGYIIEQELGNLLDFEVPFATLLTQVEVDGNDPAFQNP 120

Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180
           TKPIGPVYS+ +AERLAAEK W+IAPDGDKFRRVV SPRPKRIFEIRP+KWLLEKG+IVI
Sbjct: 121 TKPIGPVYSKADAERLAAEKDWTIAPDGDKFRRVVASPRPKRIFEIRPIKWLLEKGSIVI 180

Query: 181 CAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKPT 240
           CAGGGGIPTMYD  G KL GVEAVIDKDLCS+LLA++L +D+L+IATDV+AA++D+GKPT
Sbjct: 181 CAGGGGIPTMYDADG-KLQGVEAVIDKDLCSALLAEQLESDLLVIATDVNAAFIDFGKPT 239

Query: 241 QKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTRV 300
           QKAIAQAHPDE+E+LGFAAGSMGPKVQAA EFAR TGK AVIGSL+DI AI +G+AGTR+
Sbjct: 240 QKAIAQAHPDEMEKLGFAAGSMGPKVQAACEFARNTGKVAVIGSLSDIDAIVQGQAGTRI 299

Query: 301 STRKAGIEYR 310
           ST  AGI YR
Sbjct: 300 STATAGITYR 309


Lambda     K      H
   0.317    0.136    0.393 

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: 407
Number of extensions: 12
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: 310
Length of database: 309
Length adjustment: 27
Effective length of query: 283
Effective length of database: 282
Effective search space:    79806
Effective search space used:    79806
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate AO356_05280 AO356_05280 (carbamate kinase)
to HMM TIGR00746 (arcC: carbamate kinase (EC 2.7.2.2))

# 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/TIGR00746.hmm
# target sequence database:        /tmp/gapView.31236.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00746  [M=309]
Accession:   TIGR00746
Description: arcC: carbamate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   9.3e-133  428.0   0.1     1e-132  427.8   0.1    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05280  AO356_05280 carbamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05280  AO356_05280 carbamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.8   0.1    1e-132    1e-132       1     308 [.       1     300 [.       1     301 [. 0.99

  Alignments for each domain:
  == domain 1  score: 427.8 bits;  conditional E-value: 1e-132
                                       TIGR00746   1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqne 63 
                                                     +++vvaLGGnall+rge ++a +qr+n+++a++q++k++  g++lvi+hGngPqvG l lq +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05280   1 MRIVVALGGNALLRRGEPLTAANQRSNIRTATEQIAKIHP-GNQLVIAHGNGPQVGLLSLQAA 62 
                                                     589*************************************.********************** PP

                                       TIGR00746  64 aadsvpakPldvlgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtk 126
                                                     a+ +v+++Pldvlgae++g+iGY+++q+l + l    +e ++at+ltqv+vd +D+aFqnPtk
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05280  63 AYTAVTPYPLDVLGAETEGMIGYIIEQELGNLLD---FEVPFATLLTQVEVDGNDPAFQNPTK 122
                                                     *********************************9...************************** PP

                                       TIGR00746 127 pigpfydeeeakrlaaekgailkedagrgwRrvvpsPkPkeiveaeviktLvekgvivissgG 189
                                                     pigp+y++++a+rlaaek+++++  +g+++Rrvv+sP+Pk+i+e++ ik+L+ekg ivi++gG
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05280 123 PIGPVYSKADAERLAAEKDWTIAP-DGDKFRRVVASPRPKRIFEIRPIKWLLEKGSIVICAGG 184
                                                     ************************.9************************************* PP

                                       TIGR00746 190 GGvPvvkdgke.lkGveaviDkDlasekLaeevnaDilviltdvdavyvnygkpdekkleevk 251
                                                     GG+P+++d ++ l+GveaviDkDl+s++Lae++++D lvi+tdv+a+++++gkp++k++++++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05280 185 GGIPTMYDADGkLQGVEAVIDKDLCSALLAEQLESDLLVIATDVNAAFIDFGKPTQKAIAQAH 247
                                                     ******997655*************************************************** PP

                                       TIGR00746 252 veeleelakdgefaaGsmgPkveaaiefvesrgkkaiitslekivealegkaGtvvv 308
                                                     ++e+e+l     faaGsmgPkv+aa ef++++gk a+i+sl++i ++++g+aGt+++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05280 248 PDEMEKLG----FAAGSMGPKVQAACEFARNTGKVAVIGSLSDIDAIVQGQAGTRIS 300
                                                     ********....*******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (309 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: 00:00:00.00
# Mc/sec: 10.50
//
[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:

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