Alignments for a candidate for arcC in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcC in Pseudomonas fluorescens FW300-N1B4

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate Pf1N1B4_617 Carbamate kinase (EC 2.7.2.2)

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_617
          Length = 309

 Score =  509 bits (1310), Expect = e-149
 Identities = 253/309 (81%), Positives = 283/309 (91%), Gaps = 1/309 (0%)

Query: 1   MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60
           MRIVVALGGNALLRRGEPMTADNQR N+RIA EQIAKV PGN+LVIAHGNGPQVGLL+LQ
Sbjct: 1   MRIVVALGGNALLRRGEPMTADNQRTNIRIATEQIAKVHPGNQLVIAHGNGPQVGLLSLQ 60

Query: 61  GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120
            AAY +VS YPLDVLGAETEGMIGY+IEQE+GNLL FEVPFAT+LTQVEVD  DPAFQ P
Sbjct: 61  AAAYTQVSAYPLDVLGAETEGMIGYIIEQELGNLLDFEVPFATLLTQVEVDANDPAFQAP 120

Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180
           +KPIGPVY++ EAE+LAAEKGW+IAPDGDKFRRVV SPRPKRIFEIRP+KWLLEKG+IVI
Sbjct: 121 SKPIGPVYTKAEAEKLAAEKGWAIAPDGDKFRRVVASPRPKRIFEIRPIKWLLEKGSIVI 180

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

Query: 241 QKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTRV 300
           QKAIAQAHPDE+E+LGFAAGSMGPKVQAA EFAR TGK AVIGSL+DI AI +GKAGTR+
Sbjct: 240 QKAIAQAHPDEMEKLGFAAGSMGPKVQAACEFARHTGKTAVIGSLSDIEAIVQGKAGTRI 299

Query: 301 STRKAGIEY 309
           ST   GI Y
Sbjct: 300 STATPGITY 308


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: 388
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 Pf1N1B4_617 (Carbamate kinase (EC 2.7.2.2))
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.13552.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.3e-132  426.7   0.2   2.6e-132  426.5   0.2    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_617  Carbamate kinase (EC 2.7.2.2)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_617  Carbamate kinase (EC 2.7.2.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.5   0.2  2.6e-132  2.6e-132       1     308 [.       1     300 [.       1     301 [. 0.98

  Alignments for each domain:
  == domain 1  score: 426.5 bits;  conditional E-value: 2.6e-132
                                     TIGR00746   1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaa 65 
                                                   +++vvaLGGnall+rge ++a++qr n+++a++q++k++  g++lvi+hGngPqvG l lq +a+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_617   1 MRIVVALGGNALLRRGEPMTADNQRTNIRIATEQIAKVHP-GNQLVIAHGNGPQVGLLSLQAAAY 64 
                                                   589*************************************.************************ PP

                                     TIGR00746  66 dsvpakPldvlgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigp 130
                                                    +v+a+Pldvlgae++g+iGY+++q+l + l    +e ++at+ltqv+vd++D+aFq P kpigp
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_617  65 TQVSAYPLDVLGAETEGMIGYIIEQELGNLLD---FEVPFATLLTQVEVDANDPAFQAPSKPIGP 126
                                                   *******************************9...****************************** PP

                                     TIGR00746 131 fydeeeakrlaaekgailkedagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvv 195
                                                   +y+++ea++laaekg+ ++  +g+++Rrvv+sP+Pk+i+e++ ik+L+ekg ivi++gGGG+P++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_617 127 VYTKAEAEKLAAEKGWAIAP-DGDKFRRVVASPRPKRIFEIRPIKWLLEKGSIVICAGGGGIPTM 190
                                                   ********************.9******************************************* PP

                                     TIGR00746 196 kdgke.lkGveaviDkDlasekLaeevnaDilviltdvdavyvnygkpdekkleevkveeleela 259
                                                   +  ++ l+GveaviDkDl+s++Lae++++D lvi+tdv+a+++++gkp++k++++++++e+e+l 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_617 191 YGASGkLQGVEAVIDKDLCSALLAEQLESDLLVIATDVNAAFIDFGKPTQKAIAQAHPDEMEKLG 255
                                                   976545*********************************************************** PP

                                     TIGR00746 260 kdgefaaGsmgPkveaaiefvesrgkkaiitslekivealegkaGtvvv 308
                                                       faaGsmgPkv+aa ef++ +gk+a+i+sl++i+++++gkaGt+++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_617 256 ----FAAGSMGPKVQAACEFARHTGKTAVIGSLSDIEAIVQGKAGTRIS 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 9.82
//
[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