GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Pontibacillus litoralis JSM 072002

Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.- (characterized)
to candidate WP_036833563.1 N784_RS06825 methylisocitrate lyase

Query= SwissProt::P54528
         (301 letters)



>NCBI__GCF_000775615.1:WP_036833563.1
          Length = 306

 Score =  391 bits (1005), Expect = e-114
 Identities = 194/300 (64%), Positives = 241/300 (80%)

Query: 1   MSWIVNKQSSQEELAGRFRKLMSAPDILQIPGAHDGMAALLAKEAGFSAIYLSGAAYTAS 60
           M+WIV  + +Q E A     L+    ILQIPG HDGMAA +AK+ GF AIYLSGAAYTAS
Sbjct: 1   MTWIVENRKTQVERAKELHNLIKEETILQIPGTHDGMAARIAKDVGFQAIYLSGAAYTAS 60

Query: 61  RGLPDLGIITSAEIAERAKDLVRAADLPLLVDIDTGFGGVLNAARTAREMLEARVAAVQM 120
             LPDLG+I S E+A +A++L++A+DLPL+VDIDTG+GGVLN ARTA+EM+EA VAAVQ+
Sbjct: 61  HALPDLGMIYSNEMAAKARELIQASDLPLIVDIDTGYGGVLNVARTAKEMVEAGVAAVQI 120

Query: 121 EDQQLPKKCGHLNGKQLVPIKEMAQKIKAIKQAAPSLIVVARTDARAQEGLDAAIKRSEA 180
           EDQ LPKKCGHLNGK+L+  +EM QKI+ IK A+PSL+VVARTDA+A EG++ AI R+  
Sbjct: 121 EDQHLPKKCGHLNGKKLISTEEMMQKIQTIKAASPSLLVVARTDAKATEGIEQAITRANQ 180

Query: 181 YIEAGADAIFPEALQAENEFRQFAERIPVPLLANMTEFGKTPYYRADEFEDMGFHMVIYP 240
           Y++AGADAIFPEAL +E +FR+ +E I  PLLANMTEFGKTPYY A++F   G +MVIYP
Sbjct: 181 YLQAGADAIFPEALTSEADFRRASEAIQGPLLANMTEFGKTPYYTAEQFASFGMNMVIYP 240

Query: 241 VTSLRAAAKACERMFGLMKEHGSQKEGLHDMQTRKELYDTISYYDYEALDKTIAKTVLPD 300
           VTSLR AAKA ER+F  + + G+Q   L DMQTR++LY+TI YYDYE LDKTIAKT+LP+
Sbjct: 241 VTSLRVAAKAYERIFTTILKQGTQSNMLEDMQTREQLYETIHYYDYEKLDKTIAKTILPE 300


Lambda     K      H
   0.318    0.133    0.370 

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: 318
Number of extensions: 9
Number of successful extensions: 1
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: 301
Length of database: 306
Length adjustment: 27
Effective length of query: 274
Effective length of database: 279
Effective search space:    76446
Effective search space used:    76446
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_036833563.1 N784_RS06825 (methylisocitrate lyase)
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

# 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/TIGR02317.hmm
# target sequence database:        /tmp/gapView.2742504.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02317  [M=285]
Accession:   TIGR02317
Description: prpB: methylisocitrate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-126  407.6   4.8   1.5e-126  407.4   4.8    1.0  1  NCBI__GCF_000775615.1:WP_036833563.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000775615.1:WP_036833563.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.4   4.8  1.5e-126  1.5e-126       2     284 ..      15     295 ..      14     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: 407.4 bits;  conditional E-value: 1.5e-126
                             TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaaslglPDlglttleevaeearritrvtkl 74 
                                           +k+l++l+k+e ilqipG++++++a  a+++Gf+a+YlsGaa++as +lPDlg++ ++e+a++ar++ ++++l
  NCBI__GCF_000775615.1:WP_036833563.1  15 AKELHNLIKEETILQIPGTHDGMAARIAKDVGFQAIYLSGAAYTASHALPDLGMIYSNEMAAKARELIQASDL 87 
                                           57899******************************************************************** PP

                             TIGR02317  75 pllvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfv 147
                                           pl+vD+DtG+G++lnvart ke++eagvaav+ieDq  pkkCGhl+gk+l+s+eem++ki+ ++ a    +++
  NCBI__GCF_000775615.1:WP_036833563.1  88 PLIVDIDTGYGGVLNVARTAKEMVEAGVAAVQIEDQHLPKKCGHLNGKKLISTEEMMQKIQTIKAASP--SLL 158
                                           *************************************************************9998887..9** PP

                             TIGR02317 148 liaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadelee 220
                                           ++aRtDa+a+eG+++ai Ra+ Y++aGadaif+eal+se++fr+ ++a++ pllanmtefGktp++ta+++++
  NCBI__GCF_000775615.1:WP_036833563.1 159 VVARTDAKATEGIEQAITRANQYLQAGADAIFPEALTSEADFRRASEAIQGPLLANMTEFGKTPYYTAEQFAS 231
                                           ************************************************************************* PP

                             TIGR02317 221 lgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                            g+++viyPvt+lR+a+ka e++++++ k+Gtq ++l+++qtR++lYe+++y+dyek dk+++k
  NCBI__GCF_000775615.1:WP_036833563.1 232 FGMNMVIYPVTSLRVAAKAYERIFTTILKQGTQSNMLEDMQTREQLYETIHYYDYEKLDKTIAK 295
                                           *************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (306 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: 12.36
//
[ok]

This GapMind analysis is from Sep 24 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:

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:

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:

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:

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