Alignments for a candidate for prpB in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Marinobacter adhaerens HP15

Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate GFF1975 HP15_1932 methylisocitrate lyase 2

Query= SwissProt::Q8EJW1
         (292 letters)



>FitnessBrowser__Marino:GFF1975
          Length = 295

 Score =  401 bits (1030), Expect = e-116
 Identities = 202/289 (69%), Positives = 236/289 (81%)

Query: 4   SAGLRFRQALANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANASYGLPDLGMTSM 63
           S G RFR+AL +++PLQIVGT NAY A+MAE+ G QA+YLSG GVANASYGLPDLGMTSM
Sbjct: 6   SPGARFRKALKDNQPLQIVGTINAYAAMMAEKVGHQAIYLSGGGVANASYGLPDLGMTSM 65

Query: 64  NDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEKIGVAAVHMEDQVSQKRCGH 123
           N+V+ D  RIT+AT +PLLVDIDTGWGGAFNIARTI+E E+ G AAVH+EDQV+QKRCGH
Sbjct: 66  NEVVEDVRRITAATDVPLLVDIDTGWGGAFNIARTIREMERAGAAAVHIEDQVAQKRCGH 125

Query: 124 RPNKAVVSTEEMVDRIKAAVDARTDPNFVIMARTDAVAVEGLEAGIERAKAYIAAGADMI 183
           RPNK +VS EEMVDRIKAAVDAR D +F IMARTDA   EGLEA IERAKA I AGAD I
Sbjct: 126 RPNKEIVSQEEMVDRIKAAVDAREDKDFFIMARTDAFQKEGLEAAIERAKACIEAGADGI 185

Query: 184 FAEALTELDQYRHFKAQVKAPILANMTEFGQTQLFNKEELAQAGADMVLYPLGTFRAANQ 243
           FAEA+TEL+ Y+ F   +  PILAN+TEFG T L+N++ELA+AGADMVLYPL  FRA N+
Sbjct: 186 FAEAVTELEHYKAFSEALDVPILANITEFGATPLYNRKELAEAGADMVLYPLSAFRAMNK 245

Query: 244 AALKVMQALMNDGHQRNVLDTMQTRADLYKYLGYHAFEDKLDQLFSQDK 292
           AAL V Q ++  G Q++V+D MQTR +LY +L YH FE KLDQLF Q K
Sbjct: 246 AALTVYQNILEKGDQKDVVDMMQTRMELYDFLNYHDFEQKLDQLFQQSK 294


Lambda     K      H
   0.319    0.132    0.369 

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: 302
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: 292
Length of database: 295
Length adjustment: 26
Effective length of query: 266
Effective length of database: 269
Effective search space:    71554
Effective search space used:    71554
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate GFF1975 HP15_1932 (methylisocitrate lyase 2)
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.8392.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.5e-133  429.1   4.3     4e-133  428.9   4.3    1.0  1  lcl|FitnessBrowser__Marino:GFF1975  HP15_1932 methylisocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1975  HP15_1932 methylisocitrate lyase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.9   4.3    4e-133    4e-133       2     284 ..       8     291 ..       7     292 .. 0.99

  Alignments for each domain:
  == domain 1  score: 428.9 bits;  conditional E-value: 4e-133
                           TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtklp 75 
                                         g+++r++lk +++lqi+G+ina++a++aek+G++a+YlsG+++a+ s glPDlg+t+++ev+e++rrit++t++p
  lcl|FitnessBrowser__Marino:GFF1975   8 GARFRKALKDNQPLQIVGTINAYAAMMAEKVGHQAIYLSGGGVANaSYGLPDLGMTSMNEVVEDVRRITAATDVP 82 
                                         689*****************************************989**************************** PP

                           TIGR02317  76 llvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfvlia 150
                                         llvD+DtG+G+a+n+art++e+e+ag+aavhieDqva+k+CGh+++ke+vs+eemv++ikaav+a++d+df+++a
  lcl|FitnessBrowser__Marino:GFF1975  83 LLVDIDTGWGGAFNIARTIREMERAGAAAVHIEDQVAQKRCGHRPNKEIVSQEEMVDRIKAAVDAREDKDFFIMA 157
                                         *************************************************************************** PP

                           TIGR02317 151 RtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadeleelgyki 225
                                         RtDa   eGl+aaieRaka +eaGad if+ea++++e+++ f++a++vp+lan+tefG tpl++ +el+e+g ++
  lcl|FitnessBrowser__Marino:GFF1975 158 RTDAFQKEGLEAAIERAKACIEAGADGIFAEAVTELEHYKAFSEALDVPILANITEFGATPLYNRKELAEAGADM 232
                                         *************************************************************************** PP

                           TIGR02317 226 viyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                         v+yP++a+Ra++kaa +vy+++ +kG qk+++d +qtR elY+ l+y+d+e+k+++lf+
  lcl|FitnessBrowser__Marino:GFF1975 233 VLYPLSAFRAMNKAALTVYQNILEKGDQKDVVDMMQTRMELYDFLNYHDFEQKLDQLFQ 291
                                         ********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (295 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: 00:00:00.01
# Mc/sec: 7.14
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, or view the source code.

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