Alignments for a candidate for arcC in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcC in Azospirillum brasilense Sp245

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate AZOBR_RS13245 AZOBR_RS13245 carbamate kinase

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__azobra:AZOBR_RS13245
          Length = 317

 Score =  418 bits (1074), Expect = e-121
 Identities = 214/306 (69%), Positives = 246/306 (80%), Gaps = 6/306 (1%)

Query: 1   MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60
           MR+VVALGGNALL+RGEPMTAD QR N+RIAAE +A VA  ++LVI+HGNGPQVGLLALQ
Sbjct: 1   MRVVVALGGNALLKRGEPMTADVQRRNIRIAAEAMAPVAREHQLVISHGNGPQVGLLALQ 60

Query: 61  GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120
           GAAY     YPLDVLGAETEGMIGYMIEQE+GNLLPFEVPFAT+LT VEVDG DPAF +P
Sbjct: 61  GAAYRPDEAYPLDVLGAETEGMIGYMIEQELGNLLPFEVPFATLLTMVEVDGDDPAFGDP 120

Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180
           TK +GPVY   EA+R+AAEKGW    DG  +RRVVPSP PKRIFEIRP++WLL++GTIVI
Sbjct: 121 TKFVGPVYGAAEAQRIAAEKGWVFKADGASWRRVVPSPAPKRIFEIRPIRWLLDQGTIVI 180

Query: 181 CAGGGGIPTMYDEA----GKK--LSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYV 234
           CAGGGGIPTMY  A    GK+  L GVEAVIDKDLCS LLA+EL AD+LI+ATD +A ++
Sbjct: 181 CAGGGGIPTMYQPAMHQPGKERTLVGVEAVIDKDLCSELLARELGADLLIMATDAEAVFL 240

Query: 235 DWGKPTQKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEG 294
            WG P  +AI +A PD + R  F AGSMGPKV AA  FA ATG+ A IG+LADI AI  G
Sbjct: 241 GWGTPDARAIHRASPDAMGRYSFPAGSMGPKVDAACRFATATGRTAAIGALADIPAIVRG 300

Query: 295 KAGTRV 300
           + GT +
Sbjct: 301 EKGTLI 306


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: 372
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: 317
Length adjustment: 27
Effective length of query: 283
Effective length of database: 290
Effective search space:    82070
Effective search space used:    82070
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 AZOBR_RS13245 AZOBR_RS13245 (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.10206.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-116  375.3   0.0   1.2e-116  375.1   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS13245  AZOBR_RS13245 carbamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS13245  AZOBR_RS13245 carbamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.1   0.0  1.2e-116  1.2e-116       1     307 [.       1     306 [.       1     308 [. 0.96

  Alignments for each domain:
  == domain 1  score: 375.1 bits;  conditional E-value: 1.2e-116
                                 TIGR00746   1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaadsvp 69 
                                               ++vvvaLGGnall+rge ++a+ qr+n+++aa++++ +a+  ++lvi+hGngPqvG l+lq +a+   +
  lcl|FitnessBrowser__azobra:AZOBR_RS13245   1 MRVVVALGGNALLKRGEPMTADVQRRNIRIAAEAMAPVAR-EHQLVISHGNGPQVGLLALQGAAYRPDE 68 
                                               589***********************************99.9*************************** PP

                                 TIGR00746  70 akPldvlgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeak 138
                                               a+Pldvlgae++g+iGY+++q+l + l+   +e ++at+lt v+vd +D+aF +Ptk++gp+y  +ea+
  lcl|FitnessBrowser__azobra:AZOBR_RS13245  69 AYPLDVLGAETEGMIGYMIEQELGNLLP---FEVPFATLLTMVEVDGDDPAFGDPTKFVGPVYGAAEAQ 134
                                               ****************************...************************************** PP

                                 TIGR00746 139 rlaaekgailkedagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkdgke....... 200
                                               r aaekg+ +k  +g+ wRrvvpsP Pk+i+e++ i++L+++g+ivi++gGGG+P++++ +        
  lcl|FitnessBrowser__azobra:AZOBR_RS13245 135 RIAAEKGWVFKA-DGASWRRVVPSPAPKRIFEIRPIRWLLDQGTIVICAGGGGIPTMYQPAMhqpgker 202
                                               ***********9.9******************************************9863322223335 PP

                                 TIGR00746 201 .lkGveaviDkDlasekLaeevnaDilviltdvdavyvnygkpdekkleevkveeleelakdgefaaGs 268
                                                l GveaviDkDl+se+La+e++aD l+++td++av++ +g+pd +++++++++ + ++     f aGs
  lcl|FitnessBrowser__azobra:AZOBR_RS13245 203 tLVGVEAVIDKDLCSELLARELGADLLIMATDAEAVFLGWGTPDARAIHRASPDAMGRYS----FPAGS 267
                                               5***********************************************************....***** PP

                                 TIGR00746 269 mgPkveaaiefvesrgkkaiitslekivealegkaGtvv 307
                                               mgPkv aa +f+ ++g +a i++l++i +++ g+ Gt +
  lcl|FitnessBrowser__azobra:AZOBR_RS13245 268 MGPKVDAACRFATATGRTAAIGALADIPAIVRGEKGTLI 306
                                               *************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (317 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: 11.84
//
[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