Alignments for a candidate for arcC in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcC in Sinorhizobium meliloti 1021

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate SMa0697 SMa0697 carbamate kinase

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__Smeli:SMa0697
          Length = 324

 Score =  398 bits (1023), Expect = e-116
 Identities = 196/311 (63%), Positives = 244/311 (78%), Gaps = 3/311 (0%)

Query: 1   MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60
           MR+V+ALGGNALL+RGEPMTA+ QR+N++IAAE IA +A  +++V+ HGNGPQVGLLALQ
Sbjct: 1   MRVVIALGGNALLKRGEPMTAEVQRQNIKIAAEAIAPIAAEHQIVVTHGNGPQVGLLALQ 60

Query: 61  GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120
           G+AY     YPLD+LGAETEGMIGYM+EQE+GN+LPFEVP ATILT VEVDG DP FQNP
Sbjct: 61  GSAYKPEEAYPLDILGAETEGMIGYMLEQELGNVLPFEVPLATILTMVEVDGNDPGFQNP 120

Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180
           TK +GPVY   EA  L  +KGW    DG+K+RRVV SP P+RIFE+RP++WLL+KG +VI
Sbjct: 121 TKFVGPVYDASEAGELHQQKGWVFKQDGNKWRRVVASPIPRRIFELRPIQWLLDKGAVVI 180

Query: 181 CAGGGGIPTMYDEAGKK--LSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGK 238
           CAGGGGIPTMY E GK+  L GVEAVIDKDLCS+LLA+++ AD+LI+ATD +A +  WG 
Sbjct: 181 CAGGGGIPTMY-ERGKERTLIGVEAVIDKDLCSALLARDIEADLLILATDAEAVFTGWGT 239

Query: 239 PTQKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGT 298
           P +KAI + +P  L    F AGSMGPKV+AA  F  ATG+ A IG+LADI A+   + GT
Sbjct: 240 PERKAIFKTNPRRLGEFSFPAGSMGPKVEAACHFVNATGRVAAIGALADIPAMVRAERGT 299

Query: 299 RVSTRKAGIEY 309
            +S+  + I +
Sbjct: 300 IISSSFSDITW 310


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: 398
Number of extensions: 17
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: 324
Length adjustment: 27
Effective length of query: 283
Effective length of database: 297
Effective search space:    84051
Effective search space used:    84051
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 SMa0697 SMa0697 (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.28469.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   8.6e-117  375.5   0.0   9.8e-117  375.3   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMa0697  SMa0697 carbamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMa0697  SMa0697 carbamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.3   0.0  9.8e-117  9.8e-117       1     308 [.       1     302 [.       1     303 [. 0.98

  Alignments for each domain:
  == domain 1  score: 375.3 bits;  conditional E-value: 9.8e-117
                          TIGR00746   1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaadsvpakPldvl 76 
                                        ++vv+aLGGnall+rge ++ae qr+n+++aa++++ +a+  +++v+thGngPqvG l+lq +a++  +a+Pld+l
  lcl|FitnessBrowser__Smeli:SMa0697   1 MRVVIALGGNALLKRGEPMTAEVQRQNIKIAAEAIAPIAA-EHQIVVTHGNGPQVGLLALQGSAYKPEEAYPLDIL 75 
                                        589***********************************99.9********************************** PP

                          TIGR00746  77 gaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrlaaekgailkeda 152
                                        gae++g+iGY+l+q+l ++l+   +e ++at+lt v+vd +D+ FqnPtk++gp+yd  ea +l ++kg+ +k+ +
  lcl|FitnessBrowser__Smeli:SMa0697  76 GAETEGMIGYMLEQELGNVLP---FEVPLATILTMVEVDGNDPGFQNPTKFVGPVYDASEAGELHQQKGWVFKQ-D 147
                                        *********************...**************************************************.8 PP

                          TIGR00746 153 grgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkdgke...lkGveaviDkDlasekLaeevnaDi 225
                                        g++wRrvv+sP P++i+e + i++L++kg +vi++gGGG+P++++  +   l GveaviDkDl+s++La++++aD 
  lcl|FitnessBrowser__Smeli:SMa0697 148 GNKWRRVVASPIPRRIFELRPIQWLLDKGAVVICAGGGGIPTMYERGKertLIGVEAVIDKDLCSALLARDIEADL 223
                                        99*****************************************99655466************************* PP

                          TIGR00746 226 lviltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaiefvesrgkkaiitslekivealeg 301
                                        l+++td++av++ +g+p+ k++ + ++  l e+     f aGsmgPkveaa +fv+++g  a i++l++i +++  
  lcl|FitnessBrowser__Smeli:SMa0697 224 LILATDAEAVFTGWGTPERKAIFKTNPRRLGEFS----FPAGSMGPKVEAACHFVNATGRVAAIGALADIPAMVRA 295
                                        *********************************9....************************************** PP

                          TIGR00746 302 kaGtvvv 308
                                        + Gt+++
  lcl|FitnessBrowser__Smeli:SMa0697 296 ERGTIIS 302
                                        ****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (324 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: 00:00:00.01
# Mc/sec: 6.79
//
[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