GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Bacillus altitudinis 41KF2b

Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.- (characterized)
to candidate WP_035703253.1 BA79_RS13120 methylisocitrate lyase

Query= SwissProt::P54528
         (301 letters)



>NCBI__GCF_000691145.1:WP_035703253.1
          Length = 305

 Score =  382 bits (981), Expect = e-111
 Identities = 187/298 (62%), Positives = 238/298 (79%)

Query: 3   WIVNKQSSQEELAGRFRKLMSAPDILQIPGAHDGMAALLAKEAGFSAIYLSGAAYTASRG 62
           WIVN + SQ +LA  F++ M    + QIPG HDGM+AL A++ GF  +YLSGAA+ AS+G
Sbjct: 2   WIVNDEVSQADLAAAFKEQMHKSALFQIPGVHDGMSALYARKMGFKGLYLSGAAFCASKG 61

Query: 63  LPDLGIITSAEIAERAKDLVRAADLPLLVDIDTGFGGVLNAARTAREMLEARVAAVQMED 122
           LPDLG+I S E+AE+AK+++RA+ LPLLVD+DTG+GGVLNAAR A+EM+E++VAAVQ+ED
Sbjct: 62  LPDLGMIHSTEMAEKAKEIIRASQLPLLVDMDTGYGGVLNAARAAKEMVESKVAAVQIED 121

Query: 123 QQLPKKCGHLNGKQLVPIKEMAQKIKAIKQAAPSLIVVARTDARAQEGLDAAIKRSEAYI 182
           QQ+PKKCGHLNGK LV +++M  KIKAIKQAAP+L+V+ARTDA++  G++  I R+  Y+
Sbjct: 122 QQMPKKCGHLNGKSLVSVEDMMAKIKAIKQAAPTLLVIARTDAKSVNGMEDVIHRANLYL 181

Query: 183 EAGADAIFPEALQAENEFRQFAERIPVPLLANMTEFGKTPYYRADEFEDMGFHMVIYPVT 242
           EAGADAIFPEAL    +F   +  I  PLLANMTEFGKTPYY ADEF   GF MVIYPVT
Sbjct: 182 EAGADAIFPEALITAEDFTYASNNIKGPLLANMTEFGKTPYYHADEFSMFGFQMVIYPVT 241

Query: 243 SLRAAAKACERMFGLMKEHGSQKEGLHDMQTRKELYDTISYYDYEALDKTIAKTVLPD 300
           SLR AAKA ER+F  +KE G+Q+  L DMQTRKELY+TI Y +YE +D+ +AKT+LP+
Sbjct: 242 SLRVAAKAYERLFTEIKEKGTQQGMLEDMQTRKELYETIHYDEYEEMDQHLAKTILPE 299


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: 312
Number of extensions: 8
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: 305
Length adjustment: 27
Effective length of query: 274
Effective length of database: 278
Effective search space:    76172
Effective search space used:    76172
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_035703253.1 BA79_RS13120 (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.674262.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.7e-125  402.8   3.0   4.3e-125  402.6   3.0    1.0  1  NCBI__GCF_000691145.1:WP_035703253.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691145.1:WP_035703253.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.6   3.0  4.3e-125  4.3e-125       3     284 ..      15     294 ..      13     295 .. 0.99

  Alignments for each domain:
  == domain 1  score: 402.6 bits;  conditional E-value: 4.3e-125
                             TIGR02317   3 kalrellkkedilqipGainalvallaekaGfeavYlsGaalaaslglPDlglttleevaeearritrvtklp 75 
                                           +a++e ++k+ + qipG++++++al a+k+Gf+++YlsGaa+ as glPDlg++ ++e+ae+a++i r+++lp
  NCBI__GCF_000691145.1:WP_035703253.1  15 AAFKEQMHKSALFQIPGVHDGMSALYARKMGFKGLYLSGAAFCASKGLPDLGMIHSTEMAEKAKEIIRASQLP 87 
                                           689********************************************************************** PP

                             TIGR02317  76 llvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfvl 148
                                           llvD+DtG+G++ln+ar+ ke++e++vaav+ieDq++pkkCGhl+gk+lvs e+m++kika+++a     +++
  NCBI__GCF_000691145.1:WP_035703253.1  88 LLVDMDTGYGGVLNAARAAKEMVESKVAAVQIEDQQMPKKCGHLNGKSLVSVEDMMAKIKAIKQAAP--TLLV 158
                                           *****************************************************************98..9*** PP

                             TIGR02317 149 iaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadeleel 221
                                           iaRtDa++v+G+++ i+Ra++Y+eaGadaif+eal ++e+f + ++++k pllanmtefGktp++ ade++  
  NCBI__GCF_000691145.1:WP_035703253.1 159 IARTDAKSVNGMEDVIHRANLYLEAGADAIFPEALITAEDFTYASNNIKGPLLANMTEFGKTPYYHADEFSMF 231
                                           ************************************************************************* PP

                             TIGR02317 222 gykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                           g+++viyPvt+lR+a+ka e++++e+k+kGtq+++l+++qtRkelYe+++y++ye++d++l+k
  NCBI__GCF_000691145.1:WP_035703253.1 232 GFQMVIYPVTSLRVAAKAYERLFTEIKEKGTQQGMLEDMQTRKELYETIHYDEYEEMDQHLAK 294
                                           ************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (305 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: 00:00:00.00
# Mc/sec: 15.78
//
[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