Alignments for a candidate for L-LDH in Streptococcus oralis 7747

GapMind for catabolism of small carbon sources

Alignments for a candidate for L-LDH in Streptococcus oralis 7747

Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_038806036.1 HK29_RS04125 L-lactate dehydrogenase

Query= BRENDA::P26283
         (328 letters)



>NCBI__GCF_000382825.1:WP_038806036.1
          Length = 328

 Score =  578 bits (1490), Expect = e-170
 Identities = 290/328 (88%), Positives = 312/328 (95%)

Query: 1   MTATKQHKKVILVGDGAVGSSYAFALVNQGIAQELGIIEIPQLFEKAVGDALDLSHALAF 60
           MT+TKQHKKVILVGDGAVGSSYAFALVNQGIAQELGIIEIPQL EKAVGDALDLSHALAF
Sbjct: 1   MTSTKQHKKVILVGDGAVGSSYAFALVNQGIAQELGIIEIPQLHEKAVGDALDLSHALAF 60

Query: 61  TSPKKIYAAKYEDCADADLVVITAGAPQKPGETRLDLVGKNLAINKSIVTQVIESGFNGI 120
           TSPKKIYAA+Y DCADADLVVITAGAPQKPGETRLDLVGKNLAINKSIVTQV+ESGF+GI
Sbjct: 61  TSPKKIYAAQYSDCADADLVVITAGAPQKPGETRLDLVGKNLAINKSIVTQVVESGFDGI 120

Query: 121 FLVAANPVDILTYATWKFSGFPAEKVIGSGTSLDTARFRQALAEKLDVDARSVHAYIMGE 180
           FLVAANPVD+LTY+TWKFSGFP E+VIGSGTSLD+ARFRQALAEKLDVDARSVHAYIMGE
Sbjct: 121 FLVAANPVDVLTYSTWKFSGFPKERVIGSGTSLDSARFRQALAEKLDVDARSVHAYIMGE 180

Query: 181 HGDSEFAVWSHANVAGVNLENYLQDVQNFNGEELIDLFEGVRDAAYTIINKKGATFYGIA 240
           HGDSEFAVWSHAN+AGVNLE +L+D QN    ELI+LFEGVRDAAYTIINKKGAT+YGIA
Sbjct: 181 HGDSEFAVWSHANIAGVNLEEFLKDTQNVQEAELIELFEGVRDAAYTIINKKGATYYGIA 240

Query: 241 VALARITKAILDDENAILPLSVFQDGQYGFNEVFIGQPAIVGAHGIVRPVNIPLNDAEKQ 300
           VALARITKAILDDENA+LPLSVFQ+GQYG  +VFIGQPA+VGAHGIVRPVNIPLNDAE Q
Sbjct: 241 VALARITKAILDDENAVLPLSVFQEGQYGVKDVFIGQPAVVGAHGIVRPVNIPLNDAETQ 300

Query: 301 KMQASAKELKAIIDEAFSKEEFAAAARN 328
           KMQASAKEL+AIIDEA+   +F AA++N
Sbjct: 301 KMQASAKELQAIIDEAWKNPDFQAASKN 328


Lambda     K      H
   0.318    0.135    0.378 

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: 480
Number of extensions: 10
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: 328
Length of database: 328
Length adjustment: 28
Effective length of query: 300
Effective length of database: 300
Effective search space:    90000
Effective search space used:    90000
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: 49 (23.5 bits)

Align candidate WP_038806036.1 HK29_RS04125 (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.571518.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-129  416.8   0.1   2.9e-129  416.6   0.1    1.0  1  NCBI__GCF_000382825.1:WP_038806036.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000382825.1:WP_038806036.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.6   0.1  2.9e-129  2.9e-129       1     298 [.      12     310 ..      12     311 .. 0.98

  Alignments for each domain:
  == domain 1  score: 416.6 bits;  conditional E-value: 2.9e-129
                             TIGR01771   1 iiGagaVGssvafalltqgladelvliDine..dkaegealdlsdaasflkskvkvkagdyedlkdadlvvit 71 
                                           ++G+gaVGss+afal++qg+a+el +i i +  +ka g+aldls+a +f+ s++k++a++y+d++dadlvvit
  NCBI__GCF_000382825.1:WP_038806036.1  12 LVGDGAVGSSYAFALVNQGIAQELGIIEIPQlhEKAVGDALDLSHALAFT-SPKKIYAAQYSDCADADLVVIT 83 
                                           69**************************9743399***************.889******************* PP

                             TIGR01771  72 aGaeqkpgetRlelveknvkilksivkevvksgfdgillvvsNPvDiltyvvlklsglpkerviGsGtvLdta 144
                                           aGa+qkpgetRl+lv kn++i ksiv++vv+sgfdgi+lv++NPvD+lty ++k+sg+pkerviGsGt+Ld+a
  NCBI__GCF_000382825.1:WP_038806036.1  84 AGAPQKPGETRLDLVGKNLAINKSIVTQVVESGFDGIFLVAANPVDVLTYSTWKFSGFPKERVIGSGTSLDSA 156
                                           ************************************************************************* PP

                             TIGR01771 145 RlrrllaeklevdpksvhayvlGEHGdsevavwssakiagvplkelleekekekekelkeiekevrdaayeii 217
                                           R+r++laekl+vd++svhay++GEHGdse+avws+a+iagv+l+e+l+ +++ +e+el e+ + vrdaay ii
  NCBI__GCF_000382825.1:WP_038806036.1 157 RFRQALAEKLDVDARSVHAYIMGEHGDSEFAVWSHANIAGVNLEEFLKDTQNVQEAELIELFEGVRDAAYTII 229
                                           **************************************************999****99************** PP

                             TIGR01771 218 ekKgaTsygiglavariveailkdekrvlpvsallegeygikdvylgvPavlgknGveeilelkLseeEkekl 290
                                           +kKgaT+ygi++a+ari++ail de++vlp+s++ eg+yg+kdv++g+Pav+g++G+ + ++++L+++E++k+
  NCBI__GCF_000382825.1:WP_038806036.1 230 NKKGATYYGIAVALARITKAILDDENAVLPLSVFQEGQYGVKDVFIGQPAVVGAHGIVRPVNIPLNDAETQKM 302
                                           ************************************************************************* PP

                             TIGR01771 291 kksaetlk 298
                                           + sa+ l+
  NCBI__GCF_000382825.1:WP_038806036.1 303 QASAKELQ 310
                                           *****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (328 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 19.18
//
[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 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