Alignments for a candidate for D-LDH in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Shewanella sp. ANA-3

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate 7025755 Shewana3_2905 FAD linked oxidase domain-containing protein (RefSeq)

Query= uniprot:Q8EGS3
         (934 letters)



>FitnessBrowser__ANA3:7025755
          Length = 934

 Score = 1649 bits (4269), Expect = 0.0
 Identities = 807/934 (86%), Positives = 864/934 (92%)

Query: 1   MSINYKEVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTV 60
           MSINY  V  +L  QLG+  V++DPVRRFAWSTDASYFRIVPE+VVHA+TLEQ K TL +
Sbjct: 1   MSINYDAVYKELIQQLGESAVSNDPVRRFAWSTDASYFRIVPEIVVHADTLEQAKQTLAI 60

Query: 61  ARKHNAPVTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANA 120
           AR H  PVTFRAAGTSLSGQAIGEGILLILGHDGFR I++S D+ +ITLGAAVIG+DANA
Sbjct: 61  ARAHKVPVTFRAAGTSLSGQAIGEGILLILGHDGFRTIDISPDSNKITLGAAVIGADANA 120

Query: 121 VLAPLNRKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTG 180
            L PLN+KIGPDPAT+ASA +GGIV+NNASGMCCGTAQNSYQTIASAKLLFADGTEL+TG
Sbjct: 121 ALKPLNKKIGPDPATLASAMVGGIVSNNASGMCCGTAQNSYQTIASAKLLFADGTELNTG 180

Query: 181 CEKSKAEFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPF 240
           C+KSKA F ++HG LL  L+ L+ LTR N  LA+RIRKKYSIKNTTGY IN+L+DF DPF
Sbjct: 181 CDKSKAAFTQSHGDLLDSLASLAKLTRSNEVLAQRIRKKYSIKNTTGYSINALVDFEDPF 240

Query: 241 DIINHLMVGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAE 300
           D+INHL+VG EGTLAF+ EVTYHTV+EAKFKASAMAVF NM DAA AIP I G+SV+AAE
Sbjct: 241 DLINHLIVGAEGTLAFVEEVTYHTVDEAKFKASAMAVFFNMVDAASAIPPIIGDSVAAAE 300

Query: 301 LLDWPSIKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIR 360
           LLDW SIKAVTGK GMPDWL+ELP  +AILLIESRA+DAQTLE YTQDV AKLA     R
Sbjct: 301 LLDWASIKAVTGKKGMPDWLNELPEGAAILLIESRANDAQTLESYTQDVIAKLAHIKTER 360

Query: 361 PMEFSTNPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHK 420
           P+ FS++  VY KYWAMR GLFPI+GGERPKG+SVIIEDVAF +EHLAAAA D+TELFHK
Sbjct: 361 PISFSSDANVYSKYWAMRSGLFPIIGGERPKGSSVIIEDVAFNVEHLAAAAADLTELFHK 420

Query: 421 HGYPEGCIYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTG 480
           HGYPEG IYGHALAGNFHFIITP F +QADI+RF  FM D+A+MVI+KY+GSMKAEHGTG
Sbjct: 421 HGYPEGVIYGHALAGNFHFIITPTFASQADIERFQGFMQDVAEMVIHKYDGSMKAEHGTG 480

Query: 481 RAVAPFVEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVD 540
           RAVAPFVE EWG DAYTLMK IK +FDP+G+LNPGVILNDDS +HVKNIKPCPVVDDFVD
Sbjct: 481 RAVAPFVEMEWGADAYTLMKRIKHIFDPEGLLNPGVILNDDSTVHVKNIKPCPVVDDFVD 540

Query: 541 KCIECGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAA 600
           KCIECGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAA KMRADAKYDVIDTCAA
Sbjct: 541 KCIECGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAEKMRADAKYDVIDTCAA 600

Query: 601 CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHK 660
           CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHK
Sbjct: 601 CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHK 660

Query: 661 ITGDGITNALMKTGRLISKEVPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGP 720
           ITGDGITNALMKTGRL+SKEVPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGP
Sbjct: 661 ITGDGITNALMKTGRLLSKEVPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGP 720

Query: 721 TPKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVL 780
           TPKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDV+
Sbjct: 721 TPKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVV 780

Query: 781 SKMSNGGKIPVLVDALSCTYRTLTGNPQVQITDLVEFMHDKLLDKLSINKKVNVALHLGC 840
           SKMSNGGKIPVLVDALSCTYRTLTGNPQVQITDLVEFMHDKLLDKLSINKKVNVALHLGC
Sbjct: 781 SKMSNGGKIPVLVDALSCTYRTLTGNPQVQITDLVEFMHDKLLDKLSINKKVNVALHLGC 840

Query: 841 SARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEV 900
           SARKMKLEPKMQAIA+ACS+QV KPAGI+CCGYAGEKGLYKPEINASALRNIKKLIPVE+
Sbjct: 841 SARKMKLEPKMQAIADACSSQVHKPAGIDCCGYAGEKGLYKPEINASALRNIKKLIPVEI 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: 2460
Number of extensions: 82
Number of successful extensions: 3
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