GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Lactobacillus oryzae SG293

Align L-lactate dehydrogenase; L-LDH; EC 1.1.1.27 (characterized)
to candidate WP_034526520.1 LOSG293_RS02225 L-lactate dehydrogenase

Query= SwissProt::Q59645
         (323 letters)



>NCBI__GCF_000740055.1:WP_034526520.1
          Length = 319

 Score =  506 bits (1304), Expect = e-148
 Identities = 255/317 (80%), Positives = 279/317 (88%)

Query: 1   MSNIQNHQKVVLVGDGAVGSSYAFAMAEEGIAEEFVIVDVVKVRTVGDALDLEDATPFTA 60
           M+N +  QKV+LVGDGAVGSSYAFAM  +G+AEEFVIVDVVK RT GDALDLED   FT+
Sbjct: 1   MTNAKKFQKVMLVGDGAVGSSYAFAMMHQGLAEEFVIVDVVKERTEGDALDLEDVQAFTS 60

Query: 61  PKNIYSGEYSDCKDADLVVITAGAPQKPGETRLDLVNKNLNILSTILKPVVDSGFDGIFL 120
           PKN+YSGEYSD KDADLVVITAGAPQKPGETRLDLVNKNL ILSTI+KP+VDSGFDGIFL
Sbjct: 61  PKNVYSGEYSDAKDADLVVITAGAPQKPGETRLDLVNKNLKILSTIVKPIVDSGFDGIFL 120

Query: 121 VAANPVDILTYATWKFSGFPKEKVIGSGISLDTARLRVALGKKFNVSPESVDAYILGEHG 180
           +AANPVDILTYATWKFSGFPK KVIGSG SLDTARLR ALGKKFNV P +V+AYI+GEHG
Sbjct: 121 IAANPVDILTYATWKFSGFPKNKVIGSGTSLDTARLRAALGKKFNVDPRNVEAYIMGEHG 180

Query: 181 DSEFAAYSSATIGTKPLLEIAKEEGVSTDELAEIEDSVRNKAYEIINKKGATFYGVGTAL 240
           DSEFAAY  ATIG+KPL+ IAKE GV+ DEL +IED  R+KAYEIIN+KGATFYGV TAL
Sbjct: 181 DSEFAAYDEATIGSKPLMTIAKENGVTKDELLKIEDETRHKAYEIINRKGATFYGVATAL 240

Query: 241 MRISKAILRDENAVLPVGAYMDGEYGLNDIYIGTPAVINGQGLNRVIEAPLSDDEKKKMT 300
           MRISKAILRDENAVLPVGA +DGEYGLNDI+IGTPAVIN  G+  VIE PLSD+EK KM 
Sbjct: 241 MRISKAILRDENAVLPVGAPLDGEYGLNDIFIGTPAVINANGIESVIEIPLSDEEKAKMA 300

Query: 301 DSATTLKKVLTDGLNAL 317
            SA TLKKV  DGL+AL
Sbjct: 301 ASAETLKKVTKDGLDAL 317


Lambda     K      H
   0.313    0.134    0.368 

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: 458
Number of extensions: 8
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: 323
Length of database: 319
Length adjustment: 28
Effective length of query: 295
Effective length of database: 291
Effective search space:    85845
Effective search space used:    85845
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate WP_034526520.1 LOSG293_RS02225 (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.1854677.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.5e-132  425.8   0.0   5.2e-132  425.7   0.0    1.0  1  NCBI__GCF_000740055.1:WP_034526520.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000740055.1:WP_034526520.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.7   0.0  5.2e-132  5.2e-132       1     299 []      12     308 ..      12     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 425.7 bits;  conditional E-value: 5.2e-132
                             TIGR01771   1 iiGagaVGssvafalltqgladelvliDinedkaegealdlsdaasflkskvkvkagdyedlkdadlvvitaG 73 
                                           ++G+gaVGss+afa+++qgla+e+v++D+ ++++eg+aldl+d ++f+ s+++v++g+y+d+kdadlvvitaG
  NCBI__GCF_000740055.1:WP_034526520.1  12 LVGDGAVGSSYAFAMMHQGLAEEFVIVDVVKERTEGDALDLEDVQAFT-SPKNVYSGEYSDAKDADLVVITAG 83 
                                           69**********************************************.889********************* PP

                             TIGR01771  74 aeqkpgetRlelveknvkilksivkevvksgfdgillvvsNPvDiltyvvlklsglpkerviGsGtvLdtaRl 146
                                           a+qkpgetRl+lv+kn+kil++ivk +v+sgfdgi+l+++NPvDilty+++k+sg+pk++viGsGt+LdtaRl
  NCBI__GCF_000740055.1:WP_034526520.1  84 APQKPGETRLDLVNKNLKILSTIVKPIVDSGFDGIFLIAANPVDILTYATWKFSGFPKNKVIGSGTSLDTARL 156
                                           ************************************************************************* PP

                             TIGR01771 147 rrllaeklevdpksvhayvlGEHGdsevavwssakiagvplkelleekekekekelkeiekevrdaayeiiek 219
                                           r++l++k++vdp++v+ay++GEHGdse+a++++a+i+++pl  +++e++  +++el +ie+e+r++ayeii++
  NCBI__GCF_000740055.1:WP_034526520.1 157 RAALGKKFNVDPRNVEAYIMGEHGDSEFAAYDEATIGSKPLMTIAKENGV-TKDELLKIEDETRHKAYEIINR 228
                                           *********************************************98876.666667**************** PP

                             TIGR01771 220 KgaTsygiglavariveailkdekrvlpvsallegeygikdvylgvPavlgknGveeilelkLseeEkeklkk 292
                                           KgaT+yg+++a++ri +ail+de++vlpv+a l+geyg +d+++g+Pav+++nG+e+++e++Ls+eEk+k++ 
  NCBI__GCF_000740055.1:WP_034526520.1 229 KGATFYGVATALMRISKAILRDENAVLPVGAPLDGEYGLNDIFIGTPAVINANGIESVIEIPLSDEEKAKMAA 301
                                           ************************************************************************* PP

                             TIGR01771 293 saetlkk 299
                                           saetlkk
  NCBI__GCF_000740055.1:WP_034526520.1 302 SAETLKK 308
                                           *****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (319 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: 25.24
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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