GapMind for catabolism of small carbon sources

 

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

Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate WP_011385361.1 AMB_RS15030 FAD-binding protein

Query= SwissProt::F1QXM5
         (497 letters)



>NCBI__GCF_000009985.1:WP_011385361.1
          Length = 457

 Score =  518 bits (1334), Expect = e-151
 Identities = 252/443 (56%), Positives = 324/443 (73%), Gaps = 4/443 (0%)

Query: 46  EGVSVGSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGL 105
           E  S   AVREQHG+DES     PP+ VVF +S EEV+   K C  +  P+I FGTGT L
Sbjct: 17  ERFSTAQAVREQHGKDESHFPACPPEAVVFAQSTEEVAETVKACAAHGTPVIAFGTGTSL 76

Query: 106 EGGVGALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGAD 165
           EG V AL+GGVC  +  M +V+++  ED DVTV+PGVTRK LN YLRDTGL+FP+DPGAD
Sbjct: 77  EGHVAALKGGVCIDVSGMNRVLEVRAEDLDVTVQPGVTRKQLNEYLRDTGLFFPIDPGAD 136

Query: 166 ASLCGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNL 225
           ASL GMAAT ASGTNAVRYGTMRENVL+L+VVL DG ++ TAG   R RK++AGY+LT L
Sbjct: 137 ASLGGMAATRASGTNAVRYGTMRENVLSLQVVLPDGRVIRTAG---RARKSSAGYDLTRL 193

Query: 226 FVGSEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDD 285
           FVGSEGTLGIIT+ TLRL G+PE++ +AVC FPS+++AV++ +  +Q+GVP+ARIEFLD 
Sbjct: 194 FVGSEGTLGIITELTLRLQGIPEAISAAVCPFPSIEAAVNTVILTIQSGVPVARIEFLDK 253

Query: 286 VMINACNRFNNLSYAVTPTLFLEFHGSSKSMEEQVSVTEEITRDNGGSDFAWAEDEETRS 345
           VMI A NR++   +   PTLF EFHGS  S++EQ    E I  + G   F WA   E R+
Sbjct: 254 VMIGAVNRYSKTDHREAPTLFFEFHGSPASVQEQAEKVEAIATEFGAEGFQWATGAEERT 313

Query: 346 RLWKARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVETKADLISNNITGPIAGHVGD 405
           +LW ARH+A+YA + LRPGC+A++TD CVPISRL + ++ET+ DL +  +   I GHVGD
Sbjct: 314 KLWAARHNAYYAGVGLRPGCRAWTTDACVPISRLAECLLETEEDLKTTPLISAIVGHVGD 373

Query: 406 GNFHCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALLREEVGPLA 465
           GNFH ++++DP   +E         R+ RRALAMDGTCTGEHG+G GK A L EE G  A
Sbjct: 374 GNFHVMLLVDPGKPEEAAEAERINHRIVRRALAMDGTCTGEHGVGHGKMAFLEEEYGE-A 432

Query: 466 IEVMKGLKASLDPRNLMNPGKVL 488
           ++VM+ +K ++DP  +MNPGK++
Sbjct: 433 LDVMRAVKRAIDPAGIMNPGKIV 455


Lambda     K      H
   0.319    0.135    0.399 

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: 604
Number of extensions: 18
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: 497
Length of database: 457
Length adjustment: 33
Effective length of query: 464
Effective length of database: 424
Effective search space:   196736
Effective search space used:   196736
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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