Alignments for a candidate for prpB in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Rhizorhabdus wittichii RW1

Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.- (characterized)
to candidate WP_012050964.1 SWIT_RS24205 methylisocitrate lyase

Query= SwissProt::P54528
         (301 letters)



>NCBI__GCF_000016765.1:WP_012050964.1
          Length = 307

 Score =  320 bits (821), Expect = 2e-92
 Identities = 162/301 (53%), Positives = 212/301 (70%), Gaps = 1/301 (0%)

Query: 1   MSWIVNKQSSQEELAGRFRKLMSAPDILQIPGAHDGMAALLAKEAGFSAIYLSGAAYTAS 60
           M +++  +  +E    RFR+L++ P+ILQ+PGAH+G AAL AK AGF  +YLSGAA TAS
Sbjct: 1   MPYLIADELPRESAGARFRRLLARPNILQLPGAHNGQAALQAKAAGFEGLYLSGAAMTAS 60

Query: 61  RGLPDLGIITSAEIAERAKDLVRAADLPLLVDIDTGFGGVLNAARTAREMLEARVAAVQM 120
            GLPDLGIIT  E+A   + +VRA+ LPLLVD DTG+G  LN     R   +A   AV +
Sbjct: 61  MGLPDLGIITVDEVAFFIRQIVRASGLPLLVDGDTGYGEALNVMHMVRAFEDAGAGAVHL 120

Query: 121 EDQQLPKKCGHLNGKQLVPIKEMAQKIKAIKQAAPSLIVVARTDARAQEGLDAAIKRSEA 180
           EDQ LPKKCGHLNGK+L    +MA K+ A K+AA  +++VARTDA   EG DAA+ R+  
Sbjct: 121 EDQILPKKCGHLNGKKLADAHDMAAKVAAAKKAARDIVIVARTDAAGVEGFDAAVDRARL 180

Query: 181 YIEAGADAIFPEALQAENEFRQFAERIP-VPLLANMTEFGKTPYYRADEFEDMGFHMVIY 239
           Y+EAGADAIFPEAL     F +FA  +P VPLLANMTEFG+TP++ A EFE MG+ MVI+
Sbjct: 181 YVEAGADAIFPEALNTREMFERFARAMPGVPLLANMTEFGRTPFFTASEFEAMGYRMVIW 240

Query: 240 PVTSLRAAAKACERMFGLMKEHGSQKEGLHDMQTRKELYDTISYYDYEALDKTIAKTVLP 299
           PV+SLR A KA  R++  ++  G     + +MQTR ELY+TI  + YEALD +I +T++P
Sbjct: 241 PVSSLRVANKAQARLYAAIRRDGGTHAMVDEMQTRAELYETIGLHAYEALDASIVRTIVP 300

Query: 300 D 300
           +
Sbjct: 301 E 301


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: 289
Number of extensions: 14
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: 301
Length of database: 307
Length adjustment: 27
Effective length of query: 274
Effective length of database: 280
Effective search space:    76720
Effective search space used:    76720
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_012050964.1 SWIT_RS24205 (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.2764701.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-132  426.3   1.8   2.9e-132  426.1   1.8    1.0  1  NCBI__GCF_000016765.1:WP_012050964.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016765.1:WP_012050964.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.1   1.8  2.9e-132  2.9e-132       2     284 ..      15     296 ..      14     297 .. 0.99

  Alignments for each domain:
  == domain 1  score: 426.1 bits;  conditional E-value: 2.9e-132
                             TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaaslglPDlglttleevaeearritrvtkl 74 
                                           g+++r ll++++ilq+pGa+n+ +al+a++aGfe++YlsGaa++as+glPDlg++t++eva ++r+i+r++ l
  NCBI__GCF_000016765.1:WP_012050964.1  15 GARFRRLLARPNILQLPGAHNGQAALQAKAAGFEGLYLSGAAMTASMGLPDLGIITVDEVAFFIRQIVRASGL 87 
                                           689********************************************************************** PP

                             TIGR02317  75 pllvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfv 147
                                           pllvD DtG+Gealnv+++v+ +e+ag++avh+eDq+ pkkCGhl+gk+l ++++m++k++aa+ka +  d+v
  NCBI__GCF_000016765.1:WP_012050964.1  88 PLLVDGDTGYGEALNVMHMVRAFEDAGAGAVHLEDQILPKKCGHLNGKKLADAHDMAAKVAAAKKAAR--DIV 158
                                           ********************************************************************..89* PP

                             TIGR02317 148 liaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavk.vpllanmtefGktplltadele 219
                                           ++aRtDa++veG+daa++Ra++YveaGadaif+eal+++e+f++fa+a++ vpllanmtefG+tp++ta+e+e
  NCBI__GCF_000016765.1:WP_012050964.1 159 IVARTDAAGVEGFDAAVDRARLYVEAGADAIFPEALNTREMFERFARAMPgVPLLANMTEFGRTPFFTASEFE 231
                                           **************************************************9********************** PP

                             TIGR02317 220 elgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                            +gy++vi+Pv++lR+a+ka+ ++y+ ++++G +++++d++qtR+elYe++g+++ye+ d+++++
  NCBI__GCF_000016765.1:WP_012050964.1 232 AMGYRMVIWPVSSLRVANKAQARLYAAIRRDGGTHAMVDEMQTRAELYETIGLHAYEALDASIVR 296
                                           **************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (307 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: 17.31
//
[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