Alignments for a candidate for prpB in Thiothrix lacustris DSM 21227

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Thiothrix lacustris DSM 21227

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate WP_028487610.1 Q394_RS0100850 methylisocitrate lyase

Query= reanno::pseudo6_N2E2:Pf6N2E2_6061
         (294 letters)



>NCBI__GCF_000621325.1:WP_028487610.1
          Length = 298

 Score =  405 bits (1042), Expect = e-118
 Identities = 205/289 (70%), Positives = 234/289 (80%), Gaps = 1/289 (0%)

Query: 5   TPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGITGL 64
           TPGQ+ R AV +  PLQVVG + AN A++A++ G KA+YLSGGGVAA SLG+PDLGIT L
Sbjct: 8   TPGQKLRQAVKDNTPLQVVGAVTANSAIIAEKVGHKALYLSGGGVAASSLGIPDLGITTL 67

Query: 65  DDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAKRCG 124
            DVL D +RIT V   PLLVD+DTG+G + FN+AR  + MI+ G A  HIEDQV  KRCG
Sbjct: 68  HDVLEDAKRITAVTSAPLLVDIDTGWGGT-FNIARATREMIQSGVAGFHIEDQVMQKRCG 126

Query: 125 HRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAGADM 184
           HRPNK IVS QEMVDR+K+AVDARTDDSFVIMARTDALAVEG++SA+DRA AC+EAGADM
Sbjct: 127 HRPNKAIVSLQEMVDRVKSAVDARTDDSFVIMARTDALAVEGMQSAIDRAMACVEAGADM 186

Query: 185 IFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAFRAMN 244
           IFPEA+ +LE Y  F   +K P+LANITEFGATPLYTT +LA   V LVLYPLSAFRAM 
Sbjct: 187 IFPEAMNKLEQYAEFTKVIKVPVLANITEFGATPLYTTTELAAVGVQLVLYPLSAFRAMC 246

Query: 245 KAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAK 293
           KAAENVYT +  +GTQQNVIDTMQTRMELYD I YH FEQKLD LFA K
Sbjct: 247 KAAENVYTHLLTEGTQQNVIDTMQTRMELYDTIGYHAFEQKLDQLFAEK 295


Lambda     K      H
   0.320    0.134    0.375 

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: 264
Number of extensions: 4
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: 294
Length of database: 298
Length adjustment: 26
Effective length of query: 268
Effective length of database: 272
Effective search space:    72896
Effective search space used:    72896
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_028487610.1 Q394_RS0100850 (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.65748.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-130  420.2   2.6   2.1e-130  420.0   2.6    1.0  1  NCBI__GCF_000621325.1:WP_028487610.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000621325.1:WP_028487610.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.0   2.6  2.1e-130  2.1e-130       2     284 ..      10     293 ..       9     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 420.0 bits;  conditional E-value: 2.1e-130
                             TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtk 73 
                                           g++lr+++k + +lq++Ga+ a++a+ aek+G++a+YlsG+++aa slg+PDlg+ttl++v+e+a+rit+vt+
  NCBI__GCF_000621325.1:WP_028487610.1  10 GQKLRQAVKDNTPLQVVGAVTANSAIIAEKVGHKALYLSGGGVAAsSLGIPDLGITTLHDVLEDAKRITAVTS 82 
                                           789****************************************9989************************** PP

                             TIGR02317  74 lpllvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedf 146
                                            pllvD+DtG+G+++n+ar+ +e++++gva+ hieDqv++k+CGh+++k++vs +emv+++k+av+a++d++f
  NCBI__GCF_000621325.1:WP_028487610.1  83 APLLVDIDTGWGGTFNIARATREMIQSGVAGFHIEDQVMQKRCGHRPNKAIVSLQEMVDRVKSAVDARTDDSF 155
                                           ************************************************************************* PP

                             TIGR02317 147 vliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadele 219
                                           v++aRtDa aveG+++ai+Ra a veaGad+if+ea++++e++ ef+k +kvp+lan+tefG tpl+t+ el+
  NCBI__GCF_000621325.1:WP_028487610.1 156 VIMARTDALAVEGMQSAIDRAMACVEAGADMIFPEAMNKLEQYAEFTKVIKVPVLANITEFGATPLYTTTELA 228
                                           ************************************************************************* PP

                             TIGR02317 220 elgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                            +g+++v+yP++a+Ra+ kaae+vy++l  +Gtq++++d++qtR elY+++gy+++e+k+++lf+
  NCBI__GCF_000621325.1:WP_028487610.1 229 AVGVQLVLYPLSAFRAMCKAAENVYTHLLTEGTQQNVIDTMQTRMELYDTIGYHAFEQKLDQLFA 293
                                           **************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (298 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: 22.13
//
[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