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_034526999.1 LOSG293_RS03320 L-lactate dehydrogenase

Query= SwissProt::P56511
         (320 letters)



>NCBI__GCF_000740055.1:WP_034526999.1
          Length = 310

 Score =  344 bits (883), Expect = 1e-99
 Identities = 174/304 (57%), Positives = 224/304 (73%), Gaps = 3/304 (0%)

Query: 9   KVVLVGDGAVGSSYAFAMAQQGIAEEFVIVDVVKDRTKGDALDLEDAQAFTAPKKIYSGE 68
           KV+LVGDGAVGSS+AF++ Q G  +E VIVD+ KD T GDALDLED   F+    + +G+
Sbjct: 7   KVILVGDGAVGSSFAFSILQSGGVDELVIVDIKKDHTMGDALDLEDITPFSGSATVRTGD 66

Query: 69  YSDCKDADLVVITAGAPQKPGESRLDLVNKNLNILSSIVKPVVDSGFDGIFLVAANPVDI 128
           YSD  +A +VVITAG P+KPGE+RLDLV KN  IL SI+ PVV SGF G F+V+ANPVDI
Sbjct: 67  YSDASEAQIVVITAGVPRKPGETRLDLVEKNTKILESIISPVVQSGFKGCFVVSANPVDI 126

Query: 129 LTYATWKFSGFPKERVIGSGTSLDSSRLRVALGKQFNVDPRSVDAYIMGEHGDSEFAAYS 188
           LT  T + SGFPKERVIG+GTSLDS+RL+VAL  + +VD R ++AY++GEHGDS FA + 
Sbjct: 127 LTTMTQRLSGFPKERVIGTGTSLDSARLQVALAHKLDVDVREINAYVLGEHGDSSFANFD 186

Query: 189 TATIGTRPVRDVAKEQGVSDDDLAKLEDGVRNKAYDIINLKGATFYGIGTALMRISKAIL 248
            A +    +RD+   Q ++DDDL +LE  V+ K   II  KGATFYG+  +L  I KAIL
Sbjct: 187 EAKVAGEAIRDI---QNITDDDLLELESEVKKKGGKIIGYKGATFYGVAMSLGIICKAIL 243

Query: 249 RDENAVLPVGAYMDGQYGLNDIYIGTPAIIGGTGLKQIIESPLSADELKKMQDSAATLKK 308
            +E+ VLPV A +DGQYGL +IY+GT +II G G++Q++E PLS +E KKMQ SA  + K
Sbjct: 244 MNEDLVLPVSAPLDGQYGLKNIYLGTVSIINGNGIQQVLEVPLSEEETKKMQHSAYEMNK 303

Query: 309 VLND 312
           VL +
Sbjct: 304 VLEE 307


Lambda     K      H
   0.315    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: 337
Number of extensions: 14
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: 320
Length of database: 310
Length adjustment: 27
Effective length of query: 293
Effective length of database: 283
Effective search space:    82919
Effective search space used:    82919
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_034526999.1 LOSG293_RS03320 (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.2881572.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-108  349.2   0.7   1.2e-108  349.0   0.7    1.0  1  NCBI__GCF_000740055.1:WP_034526999.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000740055.1:WP_034526999.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.0   0.7  1.2e-108  1.2e-108       1     298 [.      10     302 ..      10     303 .. 0.98

  Alignments for each domain:
  == domain 1  score: 349.0 bits;  conditional E-value: 1.2e-108
                             TIGR01771   1 iiGagaVGssvafalltqgladelvliDinedkaegealdlsdaasflkskvkvkagdyedlkdadlvvitaG 73 
                                           ++G+gaVGss+af++l++g +delv++Di++d++ g+aldl+d ++f+  +++v++gdy+d+++a++vvitaG
  NCBI__GCF_000740055.1:WP_034526999.1  10 LVGDGAVGSSFAFSILQSGGVDELVIVDIKKDHTMGDALDLEDITPFS-GSATVRTGDYSDASEAQIVVITAG 81 
                                           69**********************************************.5589******************** PP

                             TIGR01771  74 aeqkpgetRlelveknvkilksivkevvksgfdgillvvsNPvDiltyvvlklsglpkerviGsGtvLdtaRl 146
                                            + kpgetRl+lvekn+kil+si++ vv+sgf+g ++v +NPvDilt+++++lsg+pkerviG+Gt+Ld+aRl
  NCBI__GCF_000740055.1:WP_034526999.1  82 VPRKPGETRLDLVEKNTKILESIISPVVQSGFKGCFVVSANPVDILTTMTQRLSGFPKERVIGTGTSLDSARL 154
                                           ************************************************************************* PP

                             TIGR01771 147 rrllaeklevdpksvhayvlGEHGdsevavwssakiagvplkelleekekekekelkeiekevrdaayeiiek 219
                                           +++la+kl+vd ++++ayvlGEHGds++a +++ak+ag  ++++++ +    +++l e+e+ev++++ +ii  
  NCBI__GCF_000740055.1:WP_034526999.1 155 QVALAHKLDVDVREINAYVLGEHGDSSFANFDEAKVAGEAIRDIQNIT----DDDLLELESEVKKKGGKIIGY 223
                                           ********************************************9865....77889**************** PP

                             TIGR01771 220 KgaTsygiglavariveailkdekrvlpvsallegeygikdvylgvPavlgknGveeilelkLseeEkeklkk 292
                                           KgaT+yg+++++  i++ail +e+ vlpvsa l+g+yg k++ylg+ ++++ nG++++le++LseeE++k+++
  NCBI__GCF_000740055.1:WP_034526999.1 224 KGATFYGVAMSLGIICKAILMNEDLVLPVSAPLDGQYGLKNIYLGTVSIINGNGIQQVLEVPLSEEETKKMQH 296
                                           ************************************************************************* PP

                             TIGR01771 293 saetlk 298
                                           sa  ++
  NCBI__GCF_000740055.1:WP_034526999.1 297 SAYEMN 302
                                           *98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (310 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: 00:00:00.00
# Mc/sec: 20.71
//
[ok]

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

Links

Downloads

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:

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