Alignments for a candidate for arcC in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcC in Pseudomonas fluorescens FW300-N2E3

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate AO353_03480 AO353_03480 carbamate kinase

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03480
          Length = 309

 Score =  505 bits (1300), Expect = e-148
 Identities = 247/309 (79%), Positives = 285/309 (92%), Gaps = 1/309 (0%)

Query: 1   MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60
           MRIV+ALGGNALLRRGEPMTADNQR N+R+A EQIAK+ PGN+LVIAHGNGPQ+GLL+LQ
Sbjct: 1   MRIVIALGGNALLRRGEPMTADNQRGNIRVATEQIAKIHPGNQLVIAHGNGPQIGLLSLQ 60

Query: 61  GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120
            AAY  VSPYPLDVLGAET+GMIGY+IEQE+GNLL FEVPFAT+LTQVEVD  DPAFQ+P
Sbjct: 61  AAAYTSVSPYPLDVLGAETDGMIGYIIEQELGNLLDFEVPFATLLTQVEVDPNDPAFQHP 120

Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180
           +KPIGPVYS+ EAE+LAAEKGW+IAPDGDKFRRVV SP+PKRIFEIRPVKWLLEKG+IVI
Sbjct: 121 SKPIGPVYSKAEAEKLAAEKGWAIAPDGDKFRRVVASPKPKRIFEIRPVKWLLEKGSIVI 180

Query: 181 CAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKPT 240
           CAGGGGIPTMYDE  +KL GVEAVIDKDLCS+LLA++L +D+L+IATDV+AA++D+GKPT
Sbjct: 181 CAGGGGIPTMYDE-HRKLKGVEAVIDKDLCSALLAEQLESDLLVIATDVNAAFIDFGKPT 239

Query: 241 QKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTRV 300
           QKAIA+AHPD++E+L FAAGSMGPKVQAA EFAR TGK AVIGSL+DI AI +G+AGTR+
Sbjct: 240 QKAIARAHPDDIEKLDFAAGSMGPKVQAACEFARNTGKVAVIGSLSDIEAIVQGRAGTRI 299

Query: 301 STRKAGIEY 309
           ST + GI Y
Sbjct: 300 STAEPGITY 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: 402
Number of extensions: 15
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 AO353_03480 AO353_03480 (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.581.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.2e-131  423.5   0.0   2.5e-131  423.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03480  AO353_03480 carbamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03480  AO353_03480 carbamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.3   0.0  2.5e-131  2.5e-131       1     308 [.       1     300 [.       1     301 [. 0.99

  Alignments for each domain:
  == domain 1  score: 423.3 bits;  conditional E-value: 2.5e-131
                                     TIGR00746   1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaa 65 
                                                   +++v+aLGGnall+rge ++a++qr n++ a++q++k++  g++lvi+hGngPq+G l lq +a+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03480   1 MRIVIALGGNALLRRGEPMTADNQRGNIRVATEQIAKIHP-GNQLVIAHGNGPQIGLLSLQAAAY 64 
                                                   589*************************************.************************ PP

                                     TIGR00746  66 dsvpakPldvlgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigp 130
                                                    sv+++Pldvlgae++g+iGY+++q+l + l    +e ++at+ltqv+vd++D+aFq+P kpigp
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03480  65 TSVSPYPLDVLGAETDGMIGYIIEQELGNLLD---FEVPFATLLTQVEVDPNDPAFQHPSKPIGP 126
                                                   *******************************9...****************************** PP

                                     TIGR00746 131 fydeeeakrlaaekgailkedagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvv 195
                                                   +y+++ea++laaekg+ ++  +g+++Rrvv+sPkPk+i+e++ +k+L+ekg ivi++gGGG+P++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03480 127 VYSKAEAEKLAAEKGWAIAP-DGDKFRRVVASPKPKRIFEIRPVKWLLEKGSIVICAGGGGIPTM 190
                                                   ********************.9******************************************* PP

                                     TIGR00746 196 kdgke.lkGveaviDkDlasekLaeevnaDilviltdvdavyvnygkpdekkleevkveeleela 259
                                                   +d+++ lkGveaviDkDl+s++Lae++++D lvi+tdv+a+++++gkp++k++++++++++e+l 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03480 191 YDEHRkLKGVEAVIDKDLCSALLAEQLESDLLVIATDVNAAFIDFGKPTQKAIARAHPDDIEKLD 255
                                                   988755**********************************************************9 PP

                                     TIGR00746 260 kdgefaaGsmgPkveaaiefvesrgkkaiitslekivealegkaGtvvv 308
                                                       faaGsmgPkv+aa ef++++gk a+i+sl++i+++++g aGt+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03480 256 ----FAAGSMGPKVQAACEFARNTGKVAVIGSLSDIEAIVQGRAGTRIS 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.08
//
[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