Alignments for a candidate for prpB in Allochromatium vinosum DSM 180

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Allochromatium vinosum DSM 180

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate WP_012969343.1 ALVIN_RS00470 methylisocitrate lyase

Query= reanno::Cup4G11:RR42_RS11260
         (302 letters)



>NCBI__GCF_000025485.1:WP_012969343.1
          Length = 296

 Score =  421 bits (1081), Expect = e-122
 Identities = 217/293 (74%), Positives = 246/293 (83%), Gaps = 2/293 (0%)

Query: 9   ARSAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGIS 68
           A + GA+ R A+ +E PLQVVG INA HA +A+R GYRA+YLSGGGVAAGS G+PDLG++
Sbjct: 4   AMTPGAKLRLAVQEERPLQVVGAINAYHARMAERTGYRALYLSGGGVAAGSYGIPDLGMT 63

Query: 69  NLDDVLTDVRRITDVCDVPLLVDVDTGFGASAFNVARTTRSLIKFGAGAMHIEDQVGAKR 128
           +LD+VL DV RIT + D+PLLVD DTG+G  AFN+ART + LI+ GA   HIEDQV AKR
Sbjct: 64  SLDNVLEDVSRITYITDLPLLVDADTGWGG-AFNIARTVKQLIRAGAAGCHIEDQVAAKR 122

Query: 129 CGHRPGKEIVSQGEMADRIKAAVDARTDENFVIMARTDALAVEGLDKAIERAVACVEAGA 188
           CGHRPGK IVSQ EM DRIKAAVDARTD+ FVIMARTDALAVEGLD AIERA ACVEAGA
Sbjct: 123 CGHRPGKAIVSQAEMVDRIKAAVDARTDD-FVIMARTDALAVEGLDAAIERAQACVEAGA 181

Query: 189 DAIFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVLYPLSAFRA 248
           D IFPEAMT+LA Y +F  AV+VPVLANITEFGATPLFTT ELG  GVS+VLYPLSAFRA
Sbjct: 182 DMIFPEAMTELAQYERFTAAVQVPVLANITEFGATPLFTTTELGAVGVSLVLYPLSAFRA 241

Query: 249 MNKAAENVYAAIRRDGTQQNVVDTMQTRAELYESIGYHAYEQKLDALFAQGKA 301
           MNKAA NVY A+RRDGTQ NVVDTMQTR ELY+ + YH +EQKLDALFAQ ++
Sbjct: 242 MNKAALNVYQALRRDGTQANVVDTMQTRMELYDYLDYHHFEQKLDALFAQERS 294


Lambda     K      H
   0.320    0.134    0.376 

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: 311
Number of extensions: 10
Number of successful extensions: 3
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: 302
Length of database: 296
Length adjustment: 27
Effective length of query: 275
Effective length of database: 269
Effective search space:    73975
Effective search space used:    73975
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_012969343.1 ALVIN_RS00470 (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.14944.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.6e-131  422.2   2.4   5.3e-131  422.0   2.4    1.0  1  lcl|NCBI__GCF_000025485.1:WP_012969343.1  ALVIN_RS00470 methylisocitrate l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025485.1:WP_012969343.1  ALVIN_RS00470 methylisocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.0   2.4  5.3e-131  5.3e-131       2     284 ..       8     290 ..       7     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 422.0 bits;  conditional E-value: 5.3e-131
                                 TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearrit 69 
                                               g++lr ++++e +lq++Gaina++a +ae++G++a+YlsG+++aa s g+PDlg+t+l++v+e+++rit
  lcl|NCBI__GCF_000025485.1:WP_012969343.1   8 GAKLRLAVQEERPLQVVGAINAYHARMAERTGYRALYLSGGGVAAgSYGIPDLGMTSLDNVLEDVSRIT 76 
                                               6799***************************************999*********************** PP

                                 TIGR02317  70 rvtklpllvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaav 138
                                                +t+lpllvDaDtG+G+a+n+artvk+l++ag+a++hieDqva+k+CGh++gk++vs+ emv++ikaav
  lcl|NCBI__GCF_000025485.1:WP_012969343.1  77 YITDLPLLVDADTGWGGAFNIARTVKQLIRAGAAGCHIEDQVAAKRCGHRPGKAIVSQAEMVDRIKAAV 145
                                               ********************************************************************* PP

                                 TIGR02317 139 kakkdedfvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtef 207
                                               +a++ +dfv++aRtDa aveGldaaieRa+a veaGad+if+ea+++++++++f++av+vp+lan+tef
  lcl|NCBI__GCF_000025485.1:WP_012969343.1 146 DART-DDFVIMARTDALAVEGLDAAIERAQACVEAGADMIFPEAMTELAQYERFTAAVQVPVLANITEF 213
                                               ****.56************************************************************** PP

                                 TIGR02317 208 GktplltadeleelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedye 276
                                               G tpl+t+ el  +g+++v+yP++a+Ra++kaa +vy+ l+++Gtq +++d++qtR elY+ l+y+++e
  lcl|NCBI__GCF_000025485.1:WP_012969343.1 214 GATPLFTTTELGAVGVSLVLYPLSAFRAMNKAALNVYQALRRDGTQANVVDTMQTRMELYDYLDYHHFE 282
                                               ********************************************************************* PP

                                 TIGR02317 277 kkdkelfk 284
                                               +k++ lf+
  lcl|NCBI__GCF_000025485.1:WP_012969343.1 283 QKLDALFA 290
                                               ***99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (296 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: 7.10
//
[ok]

This GapMind analysis is from Sep 24 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
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