Aligments for a candidate for D-LDH in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for D-LDH in Magnetospirillum magneticum AMB-1

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate WP_011386481.1 AMB_RS20900 FAD-binding oxidoreductase

Query= uniprot:Q8EGS3
         (934 letters)



>NCBI__GCF_000009985.1:WP_011386481.1
          Length = 936

 Score =  814 bits (2102), Expect = 0.0
 Identities = 419/934 (44%), Positives = 577/934 (61%), Gaps = 7/934 (0%)

Query: 4   NYKEVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARK 63
           +Y  ++ DL   +    +  DP+RR A+ TDAS++R+VP+VV       +VK  L   R+
Sbjct: 7   DYSALLQDLTGVMPVSRLITDPLRRLAYGTDASFYRLVPQVVAEVRDEAEVKGVLAACRR 66

Query: 64  HNAPVTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLA 123
           H APVTFRAAGTSLSGQA+ + +L+ILG  G+ +  V  + K+I L   VIG++AN  LA
Sbjct: 67  HGAPVTFRAAGTSLSGQAVSDSVLMILG-TGWTQAVVEDEGKRIRLQPGVIGAEANRRLA 125

Query: 124 PLNRKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEK 183
              RKIGPDPA+I S KIGGI ANNASGMCCGT+ NSYQT+ S +L+ ADGT +DTG  +
Sbjct: 126 AFARKIGPDPASIDSCKIGGIAANNASGMCCGTSDNSYQTVMSMRLVLADGTLVDTGNPE 185

Query: 184 SKAEFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDII 243
           S A F  +H +LL  L ++    R +  LA RIR K++IKNTTGY +N+L+DFTDP DI+
Sbjct: 186 SVAAFRASHAELLSRLDDMGRRVRDDETLAGRIRHKFAIKNTTGYSLNALVDFTDPLDIL 245

Query: 244 NHLMVGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLD 303
            HLM+G EGTL FI E+TY TV E   KASA+ +F ++ +A RA+  +    VSA EL+D
Sbjct: 246 THLMIGSEGTLGFIAEITYRTVPEHAHKASALLLFPDIAEACRAVVALKQAPVSAVELMD 305

Query: 304 WPSIKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPME 363
             S++ V  KPGMP  +  L      LL+E+R + A+ L     ++   L+G   + P  
Sbjct: 306 RASLRCVEDKPGMPAQIRGLADGVTSLLVEARGETAEALAANLAEIGRVLSGVTTLFPPA 365

Query: 364 FSTNPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGY 423
           F+ +P  Y   W +RKGLFP +G  R  GT+VIIEDVAF +E LAAA  D+  L  KHGY
Sbjct: 366 FTDDPYEYGTLWKIRKGLFPALGAVRKVGTTVIIEDVAFPIESLAAATTDLEHLCRKHGY 425

Query: 424 PEGCIYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAV 483
            E  I+GHAL GN HF  T  F  + ++DR+  FMD++A++V+NKY+GS+KAEHGTGR +
Sbjct: 426 DEAIIFGHALDGNLHFTFTQDFGIKEEVDRYARFMDEVAELVVNKYDGSLKAEHGTGRNM 485

Query: 484 APFVEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCI 543
           APFVE EWG +A  LM +IK + DP G+LNPGV+L+ D   H+ N+KP P  D  VD CI
Sbjct: 486 APFVEMEWGTEATALMWDIKGLLDPLGLLNPGVLLDKDPRAHLNNLKPLPAADSLVDTCI 545

Query: 544 ECGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQL 603
           ECGFCE+ CP+  L  SPRQRI + REI R   + + +   +   D  Y  IDTCAAC L
Sbjct: 546 ECGFCERMCPSHGLTLSPRQRITSWREISRRTAANENSDELRRLYD--YQGIDTCAACGL 603

Query: 604 CTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITG 663
           C  ACPV    G+L + LR   + +    V  + ++H+GA       G     ++ ++ G
Sbjct: 604 CATACPVGIETGRLTKSLRGRRLGSGAHAVGQWASRHYGAAMAATRFGLGAAALVSRLAG 663

Query: 664 DGITNALMKTGRLIS-KEVPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGPTP 722
                A+    R +S    P      P       P+ A +G E VVYFP C  RT GP  
Sbjct: 664 PSAMAAMASGLRTLSGGRTPKLGEHLPTAADFAPPANAPSG-ERVVYFPTCAARTMGPAS 722

Query: 723 KDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSK 782
            DP+  +LP V+  +L RAG+ V+ P+   +LCCGQ +ESKG    ADAK  EL   L K
Sbjct: 723 GDPEKDSLPTVMTRVLARAGFGVVIPDGVENLCCGQAFESKGLQATADAKAAELEAALFK 782

Query: 783 MSNGGKIPVLVDALSCTYRTLTG-NPQVQITDLVEFMHDKLLDKLS-INKKVNVALHLGC 840
            S+ G++P+++DA +C +R  T    ++++ D VEF+HD  L +LS   +   V +H+ C
Sbjct: 783 ASDHGRLPIVMDASACAWRMKTYLGERLKVVDSVEFLHDAALPRLSPTPQDAPVLVHVNC 842

Query: 841 SARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEV 900
            ARK  L+ KM  +A AC+   + P  + CCG+AG+KG   PE+N  ALR++   +P   
Sbjct: 843 GARKQGLDDKMVGLAKACAKTAIVPEAVGCCGFAGDKGFTNPELNDHALRHLAPQVPQGC 902

Query: 901 KEGYYANRMCEVGLTQHSGISYRHLAYLLEECSR 934
           + GY +NR CE+GL  H+ + YR + YLL+  +R
Sbjct: 903 EAGYSSNRTCEIGLADHADVPYRSIVYLLDRTTR 936


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: 2084
Number of extensions: 70
Number of successful extensions: 9
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: 936
Length adjustment: 43
Effective length of query: 891
Effective length of database: 893
Effective search space:   795663
Effective search space used:   795663
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, or view the source code.

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