Alignments for a candidate for arcC in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcC in Dinoroseobacter shibae DFL-12

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate 3607013 Dshi_0434 carbamate kinase (RefSeq)

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__Dino:3607013
          Length = 312

 Score =  318 bits (816), Expect = 8e-92
 Identities = 176/301 (58%), Positives = 212/301 (70%), Gaps = 3/301 (0%)

Query: 1   MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVA-PGNELVIAHGNGPQVGLLAL 59
           M +V ALGGNALL+RGEP+TA+NQR NVR AA  +A++   G+ LV+ HGNGPQVGLLAL
Sbjct: 1   MLVVAALGGNALLKRGEPLTAENQRRNVREAAVALARIVRAGHRLVVTHGNGPQVGLLAL 60

Query: 60  QGAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQN 119
           QGAAY     YPLDVLGAET GMIGY+IEQE+ N L  +   AT+LTQ+ VD  D AF++
Sbjct: 61  QGAAYKPEEAYPLDVLGAETGGMIGYIIEQELENALDHDRAVATLLTQIVVDPDDLAFRD 120

Query: 120 PTKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIV 179
           P K IGPVYSR+EAE  A   GW+IA DGDK+RRVVPSP P+ I ++R ++ LLE+  IV
Sbjct: 121 PAKFIGPVYSRDEAEARAKAVGWTIAQDGDKWRRVVPSPAPQEIPDMRVIRMLLEQDVIV 180

Query: 180 ICAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKP 239
           IC GGGGIP +   A   L G+EAVIDKD  S+LLA+EL AD L++ TDVD  Y D+G  
Sbjct: 181 ICGGGGGIPVL-RRADGSLIGIEAVIDKDAASALLARELEADALLLLTDVDGVYRDFGTD 239

Query: 240 TQKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTR 299
            Q  I    P E  +L   AGSMGPK+ AA  FA A G  A IG L +   I EG+AGTR
Sbjct: 240 RQARIDSLTPGEAFKLNLPAGSMGPKMLAAARFA-AYGGLAGIGRLDEATDILEGRAGTR 298

Query: 300 V 300
           V
Sbjct: 299 V 299


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: 332
Number of extensions: 16
Number of successful extensions: 4
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: 312
Length adjustment: 27
Effective length of query: 283
Effective length of database: 285
Effective search space:    80655
Effective search space used:    80655
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 3607013 Dshi_0434 (carbamate kinase (RefSeq))
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.30173.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.4e-116  372.7   0.0   7.2e-116  372.5   0.0    1.0  1  lcl|FitnessBrowser__Dino:3607013  Dshi_0434 carbamate kinase (RefS


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607013  Dshi_0434 carbamate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.5   0.0  7.2e-116  7.2e-116       3     308 ..       3     300 ..       1     301 [. 0.97

  Alignments for each domain:
  == domain 1  score: 372.5 bits;  conditional E-value: 7.2e-116
                         TIGR00746   3 vvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaadsvpakPldvlgae 79 
                                       vv aLGGnall+rge ++ae+qr+nv++aa +l++++++g++lv+thGngPqvG l+lq +a++  +a+Pldvlgae
  lcl|FitnessBrowser__Dino:3607013   3 VVAALGGNALLKRGEPLTAENQRRNVREAAVALARIVRAGHRLVVTHGNGPQVGLLALQGAAYKPEEAYPLDVLGAE 79 
                                       7999************************************************************************* PP

                         TIGR00746  80 sqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrlaaekgailkedagrgw 156
                                       + g+iGY+++q+l+++l      + vat+ltq++vd++D aF++P k+igp+y+++ea++ a++ g+++++ +g++w
  lcl|FitnessBrowser__Dino:3607013  80 TGGMIGYIIEQELENALD---HDRAVATLLTQIVVDPDDLAFRDPAKFIGPVYSRDEAEARAKAVGWTIAQ-DGDKW 152
                                       *****************9...899**********************************************9.9**** PP

                         TIGR00746 157 RrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkd.gkelkGveaviDkDlasekLaeevnaDilviltdv 232
                                       RrvvpsP P+ei +++vi++L+e++vivi+ gGGG+Pv +  + +l G+eaviDkD as++La+e++aD+l++ltdv
  lcl|FitnessBrowser__Dino:3607013 153 RRVVPSPAPQEIPDMRVIRMLLEQDVIVICGGGGGIPVLRRaDGSLIGIEAVIDKDAASALLARELEADALLLLTDV 229
                                       **************************************9761556******************************** PP

                         TIGR00746 233 davyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaiefvesrgkkaiitslekivealegkaGtvvv 308
                                       d vy+++g++ + ++  +++ e+ +l+      aGsmgPk+ aa +f+  +g  a i++l++++++leg aGt+v+
  lcl|FitnessBrowser__Dino:3607013 230 DGVYRDFGTDRQARIDSLTPGEAFKLN----LPAGSMGPKMLAAARFAAYGG-LAGIGRLDEATDILEGRAGTRVI 300
                                       **************************9....9***************97766.7899*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (312 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 0.00s 00:00:00.00 Elapsed: 00:00:00.02
# Mc/sec: 4.80
//
[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