GapMind for catabolism of small carbon sources

 

Alignments 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.

Links

Downloads

Related tools

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:

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:

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:

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:

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