Alignments for a candidate for D-LDH in Pontibacter ramchanderi LP43

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Pontibacter ramchanderi LP43

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate WP_101446326.1 BD749_RS16365 FAD-binding oxidoreductase

Query= uniprot:Q8EGS3
         (934 letters)



>NCBI__GCF_002846395.1:WP_101446326.1
          Length = 941

 Score =  612 bits (1578), Expect = e-179
 Identities = 333/926 (35%), Positives = 516/926 (55%), Gaps = 33/926 (3%)

Query: 30  AWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFRAAGTSLSGQAIGEGILLI 89
           ++++DA ++ + P+ VV   + E++K     + +H  P+TFR AGTSLSGQ+I +GIL+ 
Sbjct: 25  SYASDAGFYYLRPKAVVQPVSEEEIKQLFAFSHQHKVPLTFRTAGTSLSGQSITDGILVD 84

Query: 90  LGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGPDPATIASAKIGGIVANNA 149
           L    + K+ V  +  Q+ +   VIG+  NA L P  RKIGPDPA+I SA +GGI++NNA
Sbjct: 85  LSQY-WNKVLVELEGAQVRVQPGVIGAIVNAHLRPYMRKIGPDPASINSAMMGGILSNNA 143

Query: 150 SGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKTHGKLLQDLSELSHLTRHN 209
           SGMCCG ++NSY T    + +  +G    T  +     F++   +L   L ++    R+N
Sbjct: 144 SGMCCGVSKNSYHTTKYIRFVLPNGLSYTTEKQIDYLRFSEECPELYLTLQKIKQQVRNN 203

Query: 210 SALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGMEGTLAFINEVTYHTVNEAK 269
             L   IR KY  KNT GY +N+ ID+  P DI+ HL++G EGTL FI E    TV +  
Sbjct: 204 PELHYLIRHKYKTKNTVGYSVNAFIDYEHPLDIMAHLLIGAEGTLGFIAEAVLQTVPDYP 263

Query: 270 FKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVTGKPGMPDWLSELPALSAI 329
            K++A+  F ++  A +AI  +      A EL+D  S++++    G+P  +  LP  +A 
Sbjct: 264 SKSTALLYFPDIYAACQAIVPLTEAGAEAVELMDRASLRSIEHMAGVPAVIKTLPETAAA 323

Query: 330 LLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVYDKYWAMRKGLFPIVGGER 389
           LL+E +A+  + ++       A       +    F+T+P      W +RKG+FP VG  R
Sbjct: 324 LLVEFQANTPEEVQQKILSFMALAPDLALLEQPVFTTDPIEQAFLWKVRKGMFPAVGAVR 383

Query: 390 PKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGHALAGNFHFIITPAFTTQA 449
             G++V++ED+A  +  L  A  D+ ELF KH Y    I+GHA  GN HF++T AF T  
Sbjct: 384 ASGSTVLLEDIAVPVAQLGDAILDLQELFRKHAYHNAIIFGHAKDGNIHFVVTQAFDTPD 443

Query: 450 DIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEWGQDAYTLMKNIKQVFDPQ 509
           ++ R+  F+ ++  +V+ KY G++KAEHGTGR +APFVE EWG + Y +MK +KQV DP+
Sbjct: 444 EVARYDRFLKEVVKLVVKKYEGALKAEHGTGRNMAPFVETEWGPEVYRIMKTLKQVVDPE 503

Query: 510 GILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKTCPTSALNFSPRQRIATLR 569
            +LNPGVI+N D N H++N+K  P V++ VD+C+ECGFCE  CP+  L  +PRQRI   R
Sbjct: 504 NLLNPGVIINHDQNAHIQNLKELPKVEEEVDRCMECGFCEHKCPSRNLTLTPRQRIVVRR 563

Query: 570 EIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTIACPVDNSMGQLVRKLRTPYISTT 629
           E+  L++ G +    ++    +YD +DTCA   LC  ACPVD + G LV++LR    S  
Sbjct: 564 ELLNLQRKGKREEHKELLNQYQYDGLDTCAVDGLCATACPVDINTGDLVKRLRRENHSEL 623

Query: 630 EQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGITNALMKTGRLISKEVPYWNPDFP 689
             +V    AK+F  V   +  G      ++K+ G    N L +    +++EV    P FP
Sbjct: 624 ANQVALMVAKNFRPVAATVKFGLHAGAGVNKLLG---ANTLSR----LTEEVKDMIPSFP 676

Query: 690 KGGKLPKPSP----------AKAGQETVVYFPACGGRTFGPTPKDPDNRTLPEVVVTLLE 739
              K   P+P          A   +  VVYFP C  RT G    +   + + +V  ++ +
Sbjct: 677 LWTKQLAPAPGITKAMANATAPVAEAAVVYFPTCISRTMGAA--ESGRKNIIDVFKSVSD 734

Query: 740 RAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKMSNGGKIPVLVDALSCT 799
           +AG     PE  +  CCGQ++ SKG  K       E I+ + + ++ G++P+++D  SCT
Sbjct: 735 KAGLKFTIPENVQGACCGQIFSSKGYSKAFAYTANETIEKVWQWTDKGRLPLVLDITSCT 794

Query: 800 YRTLTGNP-----------QVQITDLVEFMHDKLLDKLSI-NKKVNVALHLGCSARKMKL 847
           +   +  P            ++I D ++++ + +L K ++  KK +V LH  CS +KM L
Sbjct: 795 HTLQSCRPVLTAENKQKFDNIKIIDSIDYIAEFVLPKATVLRKKADVVLHPVCSLQKMGL 854

Query: 848 EPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEVKEGYYAN 907
           E +   IA   + +V  P    CCG AG++G   PE+ ASA       +     +GYY++
Sbjct: 855 EARFVGIARQLAEEVTVPMHAGCCGMAGDRGFLVPELTASATAPEAAEVRQRDYDGYYSS 914

Query: 908 -RMCEVGLTQHSGISYRHLAYLLEEC 932
            + CE+ +T+  G +Y  + YLL+EC
Sbjct: 915 AKTCEMAMTEAVGRNYDSIVYLLDEC 940


Lambda     K      H
   0.319    0.135    0.402 

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: 1895
Number of extensions: 79
Number of successful extensions: 8
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: 934
Length of database: 941
Length adjustment: 43
Effective length of query: 891
Effective length of database: 898
Effective search space:   800118
Effective search space used:   800118
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: 57 (26.6 bits)

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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