GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Skermanella stibiiresistens SB22

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate WP_084165221.1 N825_RS31190 FAD-binding oxidoreductase

Query= uniprot:Q8EGS3
         (934 letters)



>NCBI__GCF_000576635.1:WP_084165221.1
          Length = 662

 Score =  629 bits (1621), Expect = 0.0
 Identities = 317/628 (50%), Positives = 420/628 (66%), Gaps = 2/628 (0%)

Query: 16  LGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFRAAGT 75
           LG   V  DP+R  A+ TDAS++R+VP VVV  +T  ++   L   R+   PVTFRAAGT
Sbjct: 35  LGADRVILDPLRLLAYGTDASFYRLVPRVVVKVDTEREITAVLAACRRDRLPVTFRAAGT 94

Query: 76  SLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGPDPAT 135
           SLSGQA+ + +L++LG +G+ ++ V  D K I L   V+G+DAN  LA   RKIGPDPA+
Sbjct: 95  SLSGQAVTDSVLIVLG-EGWNRMVVERDGKLIRLQPGVLGADANRRLATHARKIGPDPAS 153

Query: 136 IASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKTHGKL 195
           I SAKIGGI ANN+SGMCCGT+ NSY+T+ S +LL ADGT +DTG   S   F+ +HG L
Sbjct: 154 IDSAKIGGIAANNSSGMCCGTSDNSYKTLVSMRLLLADGTLVDTGDAASLVRFSASHGVL 213

Query: 196 LQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGMEGTLA 255
           L+ L+EL   T+ N  LA RIR K++IKNTTGY IN+L+DF +P DI+ HLM+G EGTL 
Sbjct: 214 LERLAELGRATKANKELAARIRAKFAIKNTTGYSINALVDFEEPVDILQHLMIGSEGTLG 273

Query: 256 FINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVTGKPG 315
           FI E+TY TV +   KASA+ +F ++ +A RA+ L+    VSA EL+D  ++++V  KPG
Sbjct: 274 FIAEITYRTVPDHAHKASALLLFPDIGEACRAVALLKPAPVSAVELMDRAALRSVEDKPG 333

Query: 316 MPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVYDKYW 375
           MP  +  L      LL+E+RA+D   L+     +   LAG   + P  F++    + K W
Sbjct: 334 MPAEIRGLADGVTALLVETRAEDVGGLDANIAAIATVLAGVTTLGPAVFTSRADEFGKLW 393

Query: 376 AMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGHALAG 435
            +RKGLFP VG  R  GT+VIIEDVAF +E LAAA  D+  LF KHGY E  I+GHAL G
Sbjct: 394 KIRKGLFPAVGAVRKAGTTVIIEDVAFRIEDLAAATLDLQALFAKHGYHEAIIFGHALDG 453

Query: 436 NFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEWGQDA 495
           N HF+ T  F   ++++R+ AFMDD+  +V+  Y+GS+KAEHGTGR +APFVE EWG+DA
Sbjct: 454 NLHFVFTQDFAIDSEVERYAAFMDDVCKLVVETYDGSLKAEHGTGRNMAPFVEMEWGRDA 513

Query: 496 YTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKTCPTS 555
           Y LM+ IK + DP GILNPGVILNDD   H++++KP P  D  VD CIECGFCE+ CP++
Sbjct: 514 YALMREIKSLLDPLGILNPGVILNDDPKAHLRDLKPMPKADPLVDTCIECGFCERMCPSA 573

Query: 556 ALNFSPRQRIATLREIERL-EQSGDKAAAAKMRADAKYDVIDTCAACQLCTIACPVDNSM 614
            L  +PRQRI   REI RL ++ GD A   ++R    Y  ++TCAAC LC  ACPV+   
Sbjct: 574 GLTLTPRQRIVGWREISRLADEGGDTARETELRTLYDYQGLETCAACGLCATACPVEIET 633

Query: 615 GQLVRKLRTPYISTTEQKVLDFQAKHFG 642
           G L + LR    S   +++    A+HFG
Sbjct: 634 GMLTKALRGRRQSPARRRIAALAARHFG 661


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: 1444
Number of extensions: 52
Number of successful extensions: 5
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: 662
Length adjustment: 41
Effective length of query: 893
Effective length of database: 621
Effective search space:   554553
Effective search space used:   554553
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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