Alignments for a candidate for L-LDH in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for L-LDH in Rhodobacter viridis JA737

Align L-lactate dehydrogenase; L-LDH; EC 1.1.1.27 (characterized)
to candidate WP_110806898.1 C8J30_RS16270 L-lactate dehydrogenase

Query= SwissProt::P06150
         (310 letters)



>NCBI__GCF_003217355.1:WP_110806898.1
          Length = 309

 Score =  371 bits (953), Expect = e-107
 Identities = 195/308 (63%), Positives = 241/308 (78%)

Query: 1   MKVGIVGSGMVGSATAYALALLGVAREVVLVDLDRKLAQAHAEDILHATPFAHPVWVRAG 60
           MKVGIVG+GMVGSA  +A+A+ G AREVV VD +  LAQA AEDI HA PFAHPV + AG
Sbjct: 1   MKVGIVGAGMVGSAAGFAIAMRGGAREVVFVDRNAALAQAQAEDIGHAVPFAHPVKLGAG 60

Query: 61  SYGDLEGARAVVLAAGVAQRPGETRLQLLDRNAQVFAQVVPRVLEAAPEAVLLVATNPVD 120
            Y  L GA  V+LAAGVAQ+PGE+RL LL RNA+VF++V+ RV + AP+A+L+VA+NPVD
Sbjct: 61  DYEVLAGAGIVILAAGVAQKPGESRLSLLARNAEVFSEVIARVRQHAPDALLIVASNPVD 120

Query: 121 VMTQVAYRLSALPPGRVVGSGTILDTARFRALLAEHLRVAPQSVHAYVLGEHGDSEVLVW 180
           +MT+VA R S LPP RV+G+GT+LD+ARFRALLA HL VA  SVH +VLGEHGDSEVL W
Sbjct: 121 IMTEVAQRASGLPPERVIGTGTLLDSARFRALLAGHLGVAAHSVHGFVLGEHGDSEVLAW 180

Query: 181 SSAQVGGVPLLEFAEARGRALSPEDRARIDEGVRRAAYRIIEGKGATYYGIGAGLARLVR 240
           SSA+VG  PL   A   G A++ E RA+ID GVR+AAYRII GKGAT+YGIGAGLARLV+
Sbjct: 181 SSARVGAEPLDRIALQLGVAITEEVRAKIDAGVRQAAYRIIAGKGATWYGIGAGLARLVQ 240

Query: 241 AILTDEKGVYTVSAFTPEVEGVLEVSLSLPRILGAGGVEGTVYPSLSPEEREALRRSAEI 300
           AI  D++ V +VS  +PEV G+ +V+LSLPR++GA GV  T+ PSL   E  AL+RSAE+
Sbjct: 241 AIRDDQRAVMSVSIRSPEVAGIADVALSLPRVIGAAGVVSTLVPSLDDGEWAALKRSAEV 300

Query: 301 LKEAAFAL 308
           LK++   L
Sbjct: 301 LKDSTAGL 308


Lambda     K      H
   0.319    0.136    0.383 

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: 332
Number of extensions: 12
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: 310
Length of database: 309
Length adjustment: 27
Effective length of query: 283
Effective length of database: 282
Effective search space:    79806
Effective search space used:    79806
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_110806898.1 C8J30_RS16270 (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.4181642.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-102  328.2   0.0   2.8e-102  328.0   0.0    1.0  1  NCBI__GCF_003217355.1:WP_110806898.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003217355.1:WP_110806898.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.0   0.0  2.8e-102  2.8e-102       1     299 []       5     303 ..       5     303 .. 0.98

  Alignments for each domain:
  == domain 1  score: 328.0 bits;  conditional E-value: 2.8e-102
                             TIGR01771   1 iiGagaVGssvafalltqgladelvliDinedkaegealdlsdaasflkskvkvkagdyedlkdadlvvitaG 73 
                                           i+Gag+VGs++ fa++++g a+e+v +D n   a+++a d+ +a++f+ ++vk+ agdye l++a +v+++aG
  NCBI__GCF_003217355.1:WP_110806898.1   5 IVGAGMVGSAAGFAIAMRGGAREVVFVDRNAALAQAQAEDIGHAVPFA-HPVKLGAGDYEVLAGAGIVILAAG 76 
                                           8***********************************************.89********************** PP

                             TIGR01771  74 aeqkpgetRlelveknvkilksivkevvksgfdgillvvsNPvDiltyvvlklsglpkerviGsGtvLdtaRl 146
                                            +qkpge+Rl l+++n++++++++ +v ++++d++l+v+sNPvDi+t v++++sglp+erviG+Gt+Ld+aR+
  NCBI__GCF_003217355.1:WP_110806898.1  77 VAQKPGESRLSLLARNAEVFSEVIARVRQHAPDALLIVASNPVDIMTEVAQRASGLPPERVIGTGTLLDSARF 149
                                           ************************************************************************* PP

                             TIGR01771 147 rrllaeklevdpksvhayvlGEHGdsevavwssakiagvplkelleekekekekelk.eiekevrdaayeiie 218
                                           r+lla +l+v+++svh++vlGEHGdsev +wssa+++  pl++++ + + +  +e + +i+  vr+aay+ii 
  NCBI__GCF_003217355.1:WP_110806898.1 150 RALLAGHLGVAAHSVHGFVLGEHGDSEVLAWSSARVGAEPLDRIALQLGVAITEEVRaKIDAGVRQAAYRIIA 222
                                           ********************************************99999885555555*************** PP

                             TIGR01771 219 kKgaTsygiglavariveailkdekrvlpvsallegeygikdvylgvPavlgknGveeilelkLseeEkeklk 291
                                            KgaT ygig+++ar+v+ai  d+++v+ vs+   +  gi dv+l++P+v+g+ Gv ++l  +L++ E ++lk
  NCBI__GCF_003217355.1:WP_110806898.1 223 GKGATWYGIGAGLARLVQAIRDDQRAVMSVSIRSPEVAGIADVALSLPRVIGAAGVVSTLVPSLDDGEWAALK 295
                                           ************************************************************************* PP

                             TIGR01771 292 ksaetlkk 299
                                           +sae+lk+
  NCBI__GCF_003217355.1:WP_110806898.1 296 RSAEVLKD 303
                                           ******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (309 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: 15.26
//
[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 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