Alignments for a candidate for L-LDH in Clostridium kluyveri DSM 555

GapMind for catabolism of small carbon sources

Alignments for a candidate for L-LDH in Clostridium kluyveri DSM 555

Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_012101770.1 CKL_RS06800 L-lactate dehydrogenase

Query= BRENDA::B9MKZ8
         (314 letters)



>NCBI__GCF_000016505.1:WP_012101770.1
          Length = 315

 Score =  346 bits (888), Expect = e-100
 Identities = 170/309 (55%), Positives = 236/309 (76%)

Query: 6   KIVIIGTGFVGSSTAFALVDAGLATELVLIDVNRAKAEGEAMDLNHGISFVKPVKIWAGD 65
           KI I+G GFVGSSTAFA++ +GLA+E+V++D+N+AKAEGE MDL  G SFV+P+ I AGD
Sbjct: 7   KISIVGAGFVGSSTAFAIMMSGLASEIVIVDINKAKAEGEVMDLVQGESFVEPLSIKAGD 66

Query: 66  YEDCKDADIIIITAGANQKPGETRLDLTYKNAQITKSIIENIIKYTHDAILLMVTNPVDV 125
           Y+D KD++I+IITAGA Q  G+TRL+L  KN  I KSII  I+KY+ ++ILL+V+NPVDV
Sbjct: 67  YKDTKDSNIVIITAGAAQNHGQTRLELIDKNYIIFKSIIPEIVKYSPNSILLIVSNPVDV 126

Query: 126 LTYVMYKVSGLPKNQVIGSGTVLDSSRFRYLLAQHCQVDVRNVHAYILGEHGDSEIAAWS 185
           L Y+ YK+SG P ++VIGSGTVLD+SR +Y+++    VD+R+VH Y++GEHGDSEIAAWS
Sbjct: 127 LAYMTYKLSGFPSDRVIGSGTVLDTSRLKYIISNELHVDIRDVHGYVMGEHGDSEIAAWS 186

Query: 186 LTNIGGVNFMQECLLCGKNCSPEVKEQIFNKVKNAAYEIIERKGATYYAIALAVRRIVEA 245
           L +I G+   +   L  K+ S E +E+I N V+NAAYE+I RKG+TYYAIAL+++RIVEA
Sbjct: 187 LASINGIPLKEYYKLSHKDFSKEHEEKILNCVRNAAYEVINRKGSTYYAIALSIKRIVEA 246

Query: 246 IIRDENSILPVSSIVDDVYGVKDVAISLPAIINKSGVVKVFDIPLTDEEKEKLKNSAQVI 305
           + ++ENSIL  S++++  YG++ V + +P II  SGV  +  +PL   E E L+NSA+V+
Sbjct: 247 LFKNENSILTTSTLLNGEYGIEGVFMGVPCIIGSSGVKSIIQVPLNKNESEALENSARVL 306

Query: 306 KSVIESLKL 314
           K     L +
Sbjct: 307 KKTTAHLNI 315


Lambda     K      H
   0.318    0.136    0.384 

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: 341
Number of extensions: 6
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: 314
Length of database: 315
Length adjustment: 27
Effective length of query: 287
Effective length of database: 288
Effective search space:    82656
Effective search space used:    82656
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_012101770.1 CKL_RS06800 (L-lactate dehydrogenase)
to HMM TIGR01771 (L-lactate dehydrogenase (EC 1.1.1.27))

# 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/TIGR01771.hmm
# target sequence database:        /tmp/gapView.32628.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01771  [M=299]
Accession:   TIGR01771
Description: L-LDH-NAD: L-lactate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-126  406.2   2.8   4.9e-126  406.0   2.8    1.0  1  lcl|NCBI__GCF_000016505.1:WP_012101770.1  CKL_RS06800 L-lactate dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_012101770.1  CKL_RS06800 L-lactate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.0   2.8  4.9e-126  4.9e-126       1     299 []      10     308 ..      10     308 .. 0.99

  Alignments for each domain:
  == domain 1  score: 406.0 bits;  conditional E-value: 4.9e-126
                                 TIGR01771   1 iiGagaVGssvafalltqgladelvliDinedkaegealdlsdaasflkskvkvkagdyedlkdadlvv 69 
                                               i+Gag VGss+afa++++gla+e+v++Din+ kaege++dl ++ sf+ ++ ++kagdy+d+kd+++v+
  lcl|NCBI__GCF_000016505.1:WP_012101770.1  10 IVGAGFVGSSTAFAIMMSGLASEIVIVDINKAKAEGEVMDLVQGESFV-EPLSIKAGDYKDTKDSNIVI 77 
                                               8***********************************************.889***************** PP

                                 TIGR01771  70 itaGaeqkpgetRlelveknvkilksivkevvksgfdgillvvsNPvDiltyvvlklsglpkerviGsG 138
                                               itaGa+q++g+tRlel++kn+ i+ksi++e+vk+++++ill+vsNPvD+l+y+++klsg+p++rviGsG
  lcl|NCBI__GCF_000016505.1:WP_012101770.1  78 ITAGAAQNHGQTRLELIDKNYIIFKSIIPEIVKYSPNSILLIVSNPVDVLAYMTYKLSGFPSDRVIGSG 146
                                               ********************************************************************* PP

                                 TIGR01771 139 tvLdtaRlrrllaeklevdpksvhayvlGEHGdsevavwssakiagvplkelleekekekekelk.eie 206
                                               tvLdt+Rl+++++++l+vd ++vh+yv+GEHGdse+a+ws a+i+g+plke+ + ++k+ +ke++ +i 
  lcl|NCBI__GCF_000016505.1:WP_012101770.1 147 TVLDTSRLKYIISNELHVDIRDVHGYVMGEHGDSEIAAWSLASINGIPLKEYYKLSHKDFSKEHEeKIL 215
                                               ***********************************************************8888777*** PP

                                 TIGR01771 207 kevrdaayeiiekKgaTsygiglavariveailkdekrvlpvsallegeygikdvylgvPavlgknGve 275
                                               + vr+aaye+i++Kg+T+y+i+l+++rivea++k+e+++l+ s+ll+geygi++v++gvP+++g++Gv+
  lcl|NCBI__GCF_000016505.1:WP_012101770.1 216 NCVRNAAYEVINRKGSTYYAIALSIKRIVEALFKNENSILTTSTLLNGEYGIEGVFMGVPCIIGSSGVK 284
                                               ********************************************************************* PP

                                 TIGR01771 276 eilelkLseeEkeklkksaetlkk 299
                                               +i++++L+++E+e+l++sa++lkk
  lcl|NCBI__GCF_000016505.1:WP_012101770.1 285 SIIQVPLNKNESEALENSARVLKK 308
                                               **********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (315 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.77
//
[ok]

This GapMind analysis is from Sep 24 2021. 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 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