Alignments for a candidate for D-LDH in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Shewanella amazonensis SB2B

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate 6938321 Sama_2440 iron-sulfur cluster-binding protein (RefSeq)

Query= uniprot:Q8EGS3
         (934 letters)



>FitnessBrowser__SB2B:6938321
          Length = 935

 Score = 1457 bits (3771), Expect = 0.0
 Identities = 703/934 (75%), Positives = 807/934 (86%)

Query: 1   MSINYKEVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTV 60
           MS++YK VI  L+++LG + V+DDPVRRFAWSTDASYFRIVPEVVVHA++L++V+ TL +
Sbjct: 1   MSVDYKAVIEALKSRLGPQAVSDDPVRRFAWSTDASYFRIVPEVVVHADSLDEVQQTLAI 60

Query: 61  ARKHNAPVTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANA 120
           AR+H APVTFRAAGTSLSGQAIG GILL+LGHDGFR+++VSSD  +++LGAAVIG+DANA
Sbjct: 61  AREHGAPVTFRAAGTSLSGQAIGPGILLMLGHDGFRQLKVSSDGTKVSLGAAVIGADANA 120

Query: 121 VLAPLNRKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTG 180
            L  L++KIGPDPAT+ASA IGGIV NNASGMCCGTAQNSYQTI S +++ ADGT LDTG
Sbjct: 121 ALKALDKKIGPDPATLASAMIGGIVNNNASGMCCGTAQNSYQTIDSLRMVLADGTVLDTG 180

Query: 181 CEKSKAEFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPF 240
            E S+  F ++HG LL DLS L+ + + N  LA RIRKKY+IKNTTGY +N+L+DF+ PF
Sbjct: 181 SEASRQAFEQSHGALLNDLSNLAAMVKANHGLAARIRKKYAIKNTTGYSLNALVDFSCPF 240

Query: 241 DIINHLMVGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAE 300
           DIINHLMVG EGTL F+ +VTYHTV+EA+FKASAMAVF +ME+AA AIP + G+SV+AAE
Sbjct: 241 DIINHLMVGSEGTLGFVEQVTYHTVDEARFKASAMAVFFSMEEAASAIPFLIGKSVAAAE 300

Query: 301 LLDWPSIKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIR 360
           LLDW SI+AVTGK GMPDWLS LP  +AILLIESRA DA TL+ YT++V  K+A     R
Sbjct: 301 LLDWASIRAVTGKKGMPDWLSSLPEGAAILLIESRAADADTLQAYTEEVIGKIAHIPTER 360

Query: 361 PMEFSTNPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHK 420
           P+ FST+PAVY KYWAMR GLFPI+GGERPKG+SVIIEDVAFE++HLAAAA D+T LFH+
Sbjct: 361 PIVFSTDPAVYSKYWAMRSGLFPIIGGERPKGSSVIIEDVAFEVQHLAAAAKDLTALFHE 420

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

Query: 481 RAVAPFVEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVD 540
           RAVAPFVE EWG +AYTLMK+IK +FDP G+LNPGVILNDD+ +HVKNIKPCPVVDD VD
Sbjct: 481 RAVAPFVEMEWGSEAYTLMKSIKSLFDPSGLLNPGVILNDDATVHVKNIKPCPVVDDLVD 540

Query: 541 KCIECGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAA 600
           KCIECGFCEKTCPTSALN +PRQRIATLREI RLE SGD+ AA++MR  AKYDV+DTCAA
Sbjct: 541 KCIECGFCEKTCPTSALNLTPRQRIATLREISRLEASGDEEAASRMRDAAKYDVVDTCAA 600

Query: 601 CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHK 660
           CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFD LGVIHK
Sbjct: 601 CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDTLGVIHK 660

Query: 661 ITGDGITNALMKTGRLISKEVPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGP 720
           +TGD +T+ALMK GR++SKEVPYW+P FPKGG LPK  P K GQET+VYFPACGGRTFGP
Sbjct: 661 LTGDTVTSALMKVGRMVSKEVPYWDPSFPKGGALPKLPPHKVGQETLVYFPACGGRTFGP 720

Query: 721 TPKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVL 780
           TP D D R LPEVVV +LERAGYNV+ PE TR LCCGQMWESKGDFKNAD KR+ELI+ L
Sbjct: 721 TPLDKDKRPLPEVVVQVLERAGYNVVIPEHTRSLCCGQMWESKGDFKNADGKRRELIEAL 780

Query: 781 SKMSNGGKIPVLVDALSCTYRTLTGNPQVQITDLVEFMHDKLLDKLSINKKVNVALHLGC 840
              S  GK+ V+VDALSCT RTL G+P V+I DLVEF+HD +L +LSI +K  V LHLGC
Sbjct: 781 KAKSENGKLKVVVDALSCTKRTLGGDPDVEILDLVEFLHDDVLSRLSIRQKPLVTLHLGC 840

Query: 841 SARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEV 900
           SAR +K+E KMQAIA+ C+ +V KPAGIECCGYAGEKGLYKPEINASALRNIKKL+P   
Sbjct: 841 SARHLKVEAKMQAIADTCAKEVHKPAGIECCGYAGEKGLYKPEINASALRNIKKLLPAAA 900

Query: 901 KEGYYANRMCEVGLTQHSGISYRHLAYLLEECSR 934
            EGYYANRMCEVGL++HSGISYRHL YLLEECSR
Sbjct: 901 TEGYYANRMCEVGLSKHSGISYRHLVYLLEECSR 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: 2276
Number of extensions: 78
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: 935
Length adjustment: 43
Effective length of query: 891
Effective length of database: 892
Effective search space:   794772
Effective search space used:   794772
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