GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|NCBI__GCF_000009985.1:WP_011385361.1 AMB_RS15030 FAD-binding
           protein
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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