Alignments for a candidate for prpB in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Rhodomicrobium vannielii ATCC 17100

Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.- (characterized)
to candidate WP_013419462.1 RVAN_RS09205 methylisocitrate lyase

Query= SwissProt::P54528
         (301 letters)



>NCBI__GCF_000166055.1:WP_013419462.1
          Length = 302

 Score =  311 bits (797), Expect = 1e-89
 Identities = 165/290 (56%), Positives = 208/290 (71%), Gaps = 2/290 (0%)

Query: 12  EELAG-RFRKLMSAPDILQIPGAHDGMAALLAKEAGFSAIYLSGAAYTASRGLPDLGIIT 70
           ++ AG RFR+L+    IL++PGAH+GMAAL AK AGF A+YLSGAA TAS GLPDLGIIT
Sbjct: 11  DQTAGFRFRELLERRGILKLPGAHNGMAALQAKAAGFDALYLSGAAMTASMGLPDLGIIT 70

Query: 71  SAEIAERAKDLVRAADLPLLVDIDTGFGGVLNAARTAREMLEARVAAVQMEDQQLPKKCG 130
             E+A   + + R++ LPLLVD DTG+G  LN     R   +A   AV +EDQ LPKKCG
Sbjct: 71  VDEVAFFIRQIARSSGLPLLVDGDTGYGEALNVMHMVRTFEDAGAGAVHIEDQLLPKKCG 130

Query: 131 HLNGKQLVPIKEMAQKIKAIKQAAPSLIVVARTDARAQEGLDAAIKRSEAYIEAGADAIF 190
           HLN K+L   ++MA K+ A  +A   L++VARTDA A EG+DAA+ R+  Y+EAGADAIF
Sbjct: 131 HLNDKKLADARDMAAKVAAAAKARRHLVIVARTDAAASEGIDAAVARARLYVEAGADAIF 190

Query: 191 PEALQAENEFRQFAERIP-VPLLANMTEFGKTPYYRADEFEDMGFHMVIYPVTSLRAAAK 249
           PEAL +   F++FA R+P VPLLANMTEFG+TP+Y A EFE  G+ MVI+PV+SLR A K
Sbjct: 191 PEALTSAAMFQEFARRLPGVPLLANMTEFGRTPHYTAAEFEAWGYAMVIWPVSSLRVANK 250

Query: 250 ACERMFGLMKEHGSQKEGLHDMQTRKELYDTISYYDYEALDKTIAKTVLP 299
           A  +++  +   GS +  L DMQTR ELYDTI    YEALD +I +TVLP
Sbjct: 251 AQAKLYATLARDGSTEAMLPDMQTRAELYDTIGLARYEALDASIVRTVLP 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: 294
Number of extensions: 11
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: 302
Length adjustment: 27
Effective length of query: 274
Effective length of database: 275
Effective search space:    75350
Effective search space used:    75350
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_013419462.1 RVAN_RS09205 (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.486481.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.5e-132  424.8   1.4   8.6e-132  424.6   1.4    1.0  1  NCBI__GCF_000166055.1:WP_013419462.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166055.1:WP_013419462.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.6   1.4  8.6e-132  8.6e-132       3     284 ..      16     296 ..      14     297 .. 0.99

  Alignments for each domain:
  == domain 1  score: 424.6 bits;  conditional E-value: 8.6e-132
                             TIGR02317   3 kalrellkkedilqipGainalvallaekaGfeavYlsGaalaaslglPDlglttleevaeearritrvtklp 75 
                                            ++rell+++ il++pGa+n+++al+a++aGf+a+YlsGaa++as+glPDlg++t++eva ++r+i+r + lp
  NCBI__GCF_000166055.1:WP_013419462.1  16 FRFRELLERRGILKLPGAHNGMAALQAKAAGFDALYLSGAAMTASMGLPDLGIITVDEVAFFIRQIARSSGLP 88 
                                           68*********************************************************************** PP

                             TIGR02317  76 llvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfvl 148
                                           llvD DtG+Gealnv+++v+++e+ag++avhieDq+ pkkCGhl++k+l ++ +m++k++aa+ka++  ++v+
  NCBI__GCF_000166055.1:WP_013419462.1  89 LLVDGDTGYGEALNVMHMVRTFEDAGAGAVHIEDQLLPKKCGHLNDKKLADARDMAAKVAAAAKARR--HLVI 159
                                           *******************************************************************..9*** PP

                             TIGR02317 149 iaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavk.vpllanmtefGktplltadelee 220
                                           +aRtDa+a+eG+daa++Ra++YveaGadaif+eal+s+++f+efa++++ vpllanmtefG+tp +ta+e+e 
  NCBI__GCF_000166055.1:WP_013419462.1 160 VARTDAAASEGIDAAVARARLYVEAGADAIFPEALTSAAMFQEFARRLPgVPLLANMTEFGRTPHYTAAEFEA 232
                                           *************************************************9*********************** PP

                             TIGR02317 221 lgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                            gy++vi+Pv++lR+a+ka+ k+y++l ++G+++++l ++qtR+elY+++g+ +ye+ d+++++
  NCBI__GCF_000166055.1:WP_013419462.1 233 WGYAMVIWPVSSLRVANKAQAKLYATLARDGSTEAMLPDMQTRAELYDTIGLARYEALDASIVR 296
                                           *************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (302 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: 18.18
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 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