Alignments for a candidate for prpB in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Paraburkholderia phymatum STM815

Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate WP_012405890.1 BPHY_RS33385 methylisocitrate lyase

Query= SwissProt::Q8EJW1
         (292 letters)



>NCBI__GCF_000020045.1:WP_012405890.1
          Length = 297

 Score =  387 bits (993), Expect = e-112
 Identities = 195/289 (67%), Positives = 223/289 (77%)

Query: 4   SAGLRFRQALANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANASYGLPDLGMTSM 63
           SAG  FRQA+A  +PLQ+VG   AY A MAE  GF+A+YLSG GVA  S G+PDLG+++M
Sbjct: 9   SAGAAFRQAVAEGQPLQVVGAITAYAAKMAEAVGFKAVYLSGGGVAANSLGIPDLGISTM 68

Query: 64  NDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEKIGVAAVHMEDQVSQKRCGH 123
           +DVLIDA RIT AT LPLLVDIDTGWGGAFNIART++ F K GVAAVH+EDQV QKRCGH
Sbjct: 69  DDVLIDARRITDATHLPLLVDIDTGWGGAFNIARTVRSFIKAGVAAVHLEDQVGQKRCGH 128

Query: 124 RPNKAVVSTEEMVDRIKAAVDARTDPNFVIMARTDAVAVEGLEAGIERAKAYIAAGADMI 183
           RPNK VV+T+EMVDR+KAAVDARTD  FVIMARTDA A EGL+A IERA AY+ AGADMI
Sbjct: 129 RPNKEVVATQEMVDRVKAAVDARTDDQFVIMARTDAAAAEGLDAAIERAVAYVEAGADMI 188

Query: 184 FAEALTELDQYRHFKAQVKAPILANMTEFGQTQLFNKEELAQAGADMVLYPLGTFRAANQ 243
           F EA+  LD YR FKA VK PILAN+TEFG T  F   EL  A  D+ LY  G +RA N 
Sbjct: 189 FPEAMRTLDDYRKFKAAVKVPILANLTEFGTTPFFTTTELRDANVDIALYCCGAYRAMNA 248

Query: 244 AALKVMQALMNDGHQRNVLDTMQTRADLYKYLGYHAFEDKLDQLFSQDK 292
           AAL   +  M DG Q+  + TMQTR DLYKYLGYHA+EDKLD LF+ +K
Sbjct: 249 AALNFYETTMRDGTQKAAVPTMQTREDLYKYLGYHAYEDKLDALFAANK 297


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: 305
Number of extensions: 10
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: 297
Length adjustment: 26
Effective length of query: 266
Effective length of database: 271
Effective search space:    72086
Effective search space used:    72086
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 WP_012405890.1 BPHY_RS33385 (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.1867059.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.7e-129  415.1   6.5   7.7e-129  414.9   6.5    1.0  1  NCBI__GCF_000020045.1:WP_012405890.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020045.1:WP_012405890.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.9   6.5  7.7e-129  7.7e-129       2     284 ..      11     294 ..      10     295 .. 0.99

  Alignments for each domain:
  == domain 1  score: 414.9 bits;  conditional E-value: 7.7e-129
                             TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtk 73 
                                           g+a+r++++++++lq++Gai a++a +ae++Gf+avYlsG+++aa slg+PDlg++t+++v+ +arrit++t+
  NCBI__GCF_000020045.1:WP_012405890.1  11 GAAFRQAVAEGQPLQVVGAITAYAAKMAEAVGFKAVYLSGGGVAAnSLGIPDLGISTMDDVLIDARRITDATH 83 
                                           679***************************************9988*************************** PP

                             TIGR02317  74 lpllvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedf 146
                                           lpllvD+DtG+G+a+n+artv+++++agvaavh+eDqv +k+CGh+++ke+v ++emv+++kaav+a++d++f
  NCBI__GCF_000020045.1:WP_012405890.1  84 LPLLVDIDTGWGGAFNIARTVRSFIKAGVAAVHLEDQVGQKRCGHRPNKEVVATQEMVDRVKAAVDARTDDQF 156
                                           ************************************************************************* PP

                             TIGR02317 147 vliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadele 219
                                           v++aRtDa+a eGldaaieRa aYveaGad+if+ea+++++++r+f++avkvp+lan+tefG tp++t+ el+
  NCBI__GCF_000020045.1:WP_012405890.1 157 VIMARTDAAAAEGLDAAIERAVAYVEAGADMIFPEAMRTLDDYRKFKAAVKVPILANLTEFGTTPFFTTTELR 229
                                           ************************************************************************* PP

                             TIGR02317 220 elgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                           ++ ++i++y   a Ra++ aa + ye+ +++Gtqk+ + ++qtR++lY+ lgy++ye+k++ lf+
  NCBI__GCF_000020045.1:WP_012405890.1 230 DANVDIALYCCGAYRAMNAAALNFYETTMRDGTQKAAVPTMQTREDLYKYLGYHAYEDKLDALFA 294
                                           ************************************************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (297 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: 9.55
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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