Alignments for a candidate for D-LDH in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Shewanella loihica PV-4

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate 5210708 Shew_3136 FAD linked oxidase domain-containing protein (RefSeq)

Query= uniprot:Q8EGS3
         (934 letters)



>FitnessBrowser__PV4:5210708
          Length = 934

 Score = 1580 bits (4092), Expect = 0.0
 Identities = 768/934 (82%), Positives = 838/934 (89%)

Query: 1   MSINYKEVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTV 60
           MSINY  V+ DLR +LGD  V+DD VRRFAWSTDASYFRIVPEVVVHAETLE  + TL V
Sbjct: 1   MSINYSAVVADLRAKLGDEAVSDDAVRRFAWSTDASYFRIVPEVVVHAETLEDARDTLEV 60

Query: 61  ARKHNAPVTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANA 120
           AR+HNAPVTFRAAGTSLSGQAIGEGILLILGHDGFRKI VS D  QI+LGAAVIG DAN 
Sbjct: 61  ARQHNAPVTFRAAGTSLSGQAIGEGILLILGHDGFRKIAVSEDHNQISLGAAVIGGDANL 120

Query: 121 VLAPLNRKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTG 180
            L P N+KIGPDPAT+ASA +GGIV+NNASGMCCGTAQNSYQTIASAKLLFADGT LDTG
Sbjct: 121 ALKPFNKKIGPDPATLASAMVGGIVSNNASGMCCGTAQNSYQTIASAKLLFADGTRLDTG 180

Query: 181 CEKSKAEFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPF 240
           CE+SK  F ++H +LL +L++L+ LT  N  LA+RIRKKYSIKNTTGY IN+L+DF DPF
Sbjct: 181 CERSKEAFRESHQQLLSELTDLAKLTASNPVLADRIRKKYSIKNTTGYSINALVDFEDPF 240

Query: 241 DIINHLMVGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAE 300
           ++INHL+VG EGTLAF+ EVTY+TV+EAKFKASAMAVF NMEDAARAIP I  +SV+AAE
Sbjct: 241 ELINHLIVGAEGTLAFVEEVTYNTVDEAKFKASAMAVFFNMEDAARAIPPIKCDSVAAAE 300

Query: 301 LLDWPSIKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIR 360
           LLDW SIKAVTGK GMPDWLSELP  +AILLIESRA+D  TL+ YTQDV AKLA  +  R
Sbjct: 301 LLDWASIKAVTGKKGMPDWLSELPEGAAILLIESRANDEATLDAYTQDVIAKLAHIETER 360

Query: 361 PMEFSTNPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHK 420
           P+ FS +P VY KYWAMR GLFPI+GGERPKGTSVIIEDVAFELEHLA AA D+T LFHK
Sbjct: 361 PISFSRDPEVYSKYWAMRSGLFPIIGGERPKGTSVIIEDVAFELEHLANAATDLTALFHK 420

Query: 421 HGYPEGCIYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTG 480
           HGYPEG IYGHALAGNFHFIITP F +Q DIDRFH FM D+A+MVINKY+GSMKAEHGTG
Sbjct: 421 HGYPEGVIYGHALAGNFHFIITPTFASQEDIDRFHGFMQDVAEMVINKYDGSMKAEHGTG 480

Query: 481 RAVAPFVEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVD 540
           RAVAPFVE EWG DAYTLMK IKQ+FDPQG+LNPGVILNDD+N+HVKNIKPCPVVDDFVD
Sbjct: 481 RAVAPFVEMEWGADAYTLMKRIKQIFDPQGLLNPGVILNDDANVHVKNIKPCPVVDDFVD 540

Query: 541 KCIECGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAA 600
           +CIECGFCEKTCPTSALNF+PRQRIATLREI RLE SGDK AA +MRA AKYDV+DTCAA
Sbjct: 541 RCIECGFCEKTCPTSALNFTPRQRIATLREIARLEASGDKQAAEEMRAAAKYDVVDTCAA 600

Query: 601 CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHK 660
           CQLCTIACPVDNSMGQLVRKLRTPYI+TTEQKVLDFQAKHFGAVNQVISTGFDVL +IHK
Sbjct: 601 CQLCTIACPVDNSMGQLVRKLRTPYITTTEQKVLDFQAKHFGAVNQVISTGFDVLSIIHK 660

Query: 661 ITGDGITNALMKTGRLISKEVPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGP 720
           +TGD +TN LMK GR++SKEVPYWNPDF KGGKLPKPSPA   +ETVVYFPACGGRTFGP
Sbjct: 661 VTGDSVTNGLMKVGRMVSKEVPYWNPDFAKGGKLPKPSPASPDKETVVYFPACGGRTFGP 720

Query: 721 TPKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVL 780
           TPKDPDNRTLPEVVVTLLERAGYNV+TP+ TR LCCGQMWESKGDFKNADAKR ELID L
Sbjct: 721 TPKDPDNRTLPEVVVTLLERAGYNVVTPDNTRHLCCGQMWESKGDFKNADAKRDELIDAL 780

Query: 781 SKMSNGGKIPVLVDALSCTYRTLTGNPQVQITDLVEFMHDKLLDKLSINKKVNVALHLGC 840
           S +S+ GK+PV+VDALSCTYRTLTGNP+V+ITDLVEFMHDK+L KL+  KKVNVALHLGC
Sbjct: 781 SALSDNGKVPVVVDALSCTYRTLTGNPKVEITDLVEFMHDKILPKLTFTKKVNVALHLGC 840

Query: 841 SARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEV 900
           SARKMKLEPKMQA+A+ACS  V  P GIECCGYAGEKGLYKPEINASALRNIKKLIPV++
Sbjct: 841 SARKMKLEPKMQALADACSNGVKLPEGIECCGYAGEKGLYKPEINASALRNIKKLIPVDI 900

Query: 901 KEGYYANRMCEVGLTQHSGISYRHLAYLLEECSR 934
           KEGYYANRMCEVGLTQHSGISYRHLAYLLEECSR
Sbjct: 901 KEGYYANRMCEVGLTQHSGISYRHLAYLLEECSR 934


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: 2401
Number of extensions: 83
Number of successful extensions: 4
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: 934
Length adjustment: 43
Effective length of query: 891
Effective length of database: 891
Effective search space:   793881
Effective search space used:   793881
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 17 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