Alignments for a candidate for D-LDH in Photobacterium gaetbulicola Gung47

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Photobacterium gaetbulicola Gung47

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate WP_044623066.1 H744_RS17000 FAD-binding oxidoreductase

Query= uniprot:Q8EGS3
         (934 letters)



>NCBI__GCF_000940995.1:WP_044623066.1
          Length = 949

 Score =  779 bits (2012), Expect = 0.0
 Identities = 404/950 (42%), Positives = 586/950 (61%), Gaps = 19/950 (2%)

Query: 1   MSINYKEVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTV 60
           M   Y+++   L TQ+ +  +  +  +R A+ TDAS++R++P++V+    L++V  T+  
Sbjct: 1   MENKYRQLEALLATQIDEARIITEEAKRLAYGTDASFYRLIPKLVLRLNNLDEVIFTIQS 60

Query: 61  ARKHNAPVTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANA 120
             + + P TFRAAGTSLSGQAI + +L+ L  D +R   +    ++I L   VIG+DAN 
Sbjct: 61  CCQLSIPFTFRAAGTSLSGQAISDSVLITLS-DKWRGHCILDQGEKIRLQPGVIGADANR 119

Query: 121 VLAPLNRKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTG 180
            LAP  RKIGPDPA+I + KIGGI ANNASGMCCGTAQNSY T+ S  ++F DGT LDT 
Sbjct: 120 YLAPYQRKIGPDPASINTCKIGGIAANNASGMCCGTAQNSYNTVNSMTIVFTDGTVLDTA 179

Query: 181 CEKSKAEFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPF 240
            E S   F      L++ L++L   T+ N+ L+E+IR KY +KNTTGY +N+L+D+ DP 
Sbjct: 180 SEASIEAFKNKRPDLIEGLAQLVEETQQNTELSEKIRHKYRLKNTTGYALNALVDYHDPV 239

Query: 241 DIINHLMVGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAE 300
           D+I HLM+G EGTL FI ++TY+TV E   KAS + VF ++E A++A+ ++    VSA E
Sbjct: 240 DVIEHLMIGSEGTLGFIADITYNTVIEHPHKASTLLVFGDIETASQAVSVLANTHVSAVE 299

Query: 301 LLDWPSIKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIR 360
           ++D  ++++V  KPGMPD++  L   SA LLIE+RA  +  L     +V + L  F    
Sbjct: 300 MMDGRALRSVADKPGMPDYIQALDLESAALLIETRASCSHQLGQQCVEVMSALEDFTITH 359

Query: 361 PMEFSTNPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHK 420
              F+T+       WA+RKG+FP VG  R  GT+VIIEDVAF +EHLA    ++ +LF K
Sbjct: 360 STPFTTDATTIASLWAIRKGMFPAVGAVRETGTTVIIEDVAFPVEHLAMGVRELQQLFDK 419

Query: 421 HGYPEGCIYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTG 480
           + Y E  I+GHAL GN HF+ T  F   A+++R+ +FMDD+A++V  KY GS+KAEHGTG
Sbjct: 420 YHYGEAIIFGHALEGNLHFVFTQGFEDGAEVNRYGSFMDDVAELVAVKYQGSLKAEHGTG 479

Query: 481 RAVAPFVEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVD 540
           R +AP+VE EWG D Y LMK IK +FDP+G+LNPGVI+NDD+  H+ ++KP P  D+ +D
Sbjct: 480 RNMAPYVELEWGHDGYRLMKQIKALFDPEGLLNPGVIINDDTRAHISHLKPMPAADELID 539

Query: 541 KCIECGFCEKTCPTSALNFSPRQRIATLREIERLEQ-----SGDKAAAAKMRADAKYDVI 595
           +CIECGFCE  CP+  L  SPRQRI   RE++  E+     +  +    +++   +Y  I
Sbjct: 540 RCIECGFCEPVCPSRTLTLSPRQRIVLYRELQHRERQYLAGNSRRPPVDELKQIFEYQGI 599

Query: 596 DTCAACQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVL 655
           DTCAA  LC   CPV  + G LV+KLR          +  + A HFGA   ++  G    
Sbjct: 600 DTCAATGLCADRCPVGINTGDLVKKLRVDKYQRF-TPIARWTADHFGATTTMVKAGLKSN 658

Query: 656 GVIHKITGDGITNALMKTGRLISK-EVPYWNPDFPKGG--KLPKP-------SPAKAGQE 705
            +  K+ GD +   +    R ++K   P W P++P+    KL +          A+   +
Sbjct: 659 QLARKLVGDKVVGTITNGLRKMTKGATPIWIPEYPQSNPHKLSQSLSTTAHRVQAENSDK 718

Query: 706 TVVYFPACGGRTFGPTPKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGD 765
            VVY P+C  R  G      D+R L EV ++LL++AG+ VITPEK    CCG  ++SKG 
Sbjct: 719 RVVYLPSCASRAMGQQDSAKDSRPLTEVTLSLLKKAGFEVITPEKLSSQCCGMPYDSKGM 778

Query: 766 FKNADAKRQELIDVLSKMSNGGKIPVLVDALSCTYRTLTGNPQ-VQITDLVEFMHDKLLD 824
              A+ K +EL  +L + S  G  PVL+D   C  R++    Q +++ + V F+   LL 
Sbjct: 779 NDIANQKAKELESLLWEASKEGAYPVLMDTSPCAKRSIENFTQPLEVLEPVGFVSRYLLP 838

Query: 825 KLSINK-KVNVALHLGCSARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPE 883
            LS++  K  V LH+ CS+R+M LE  M ++A AC+  V+ P  I+CCG+AG+KG   PE
Sbjct: 839 HLSLSPIKETVMLHVTCSSRRMGLEADMLSLAKACAETVVLPEHIQCCGWAGDKGFTTPE 898

Query: 884 INASALRNIKKLIPVEVKEGYYANRMCEVGLTQHSGISYRHLAYLLEECS 933
           +N +A+  +K+ +P     G+  +R CE+GL+ HSGI Y+ + YL++E +
Sbjct: 899 LNEAAVAPLKEQVPANCTRGFSNSRTCEIGLSHHSGIPYQSILYLVDEAA 948


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: 1945
Number of extensions: 82
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: 949
Length adjustment: 44
Effective length of query: 890
Effective length of database: 905
Effective search space:   805450
Effective search space used:   805450
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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