Alignments for a candidate for edd in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Magnetospirillum magneticum AMB-1

Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate WP_011384917.1 AMB_RS12770 dihydroxy-acid dehydratase

Query= SwissProt::P21909
         (607 letters)



>NCBI__GCF_000009985.1:WP_011384917.1
          Length = 616

 Score =  211 bits (536), Expect = 1e-58
 Identities = 178/588 (30%), Positives = 266/588 (45%), Gaps = 62/588 (10%)

Query: 64  DFNRMNIGVVTSYNDMLSAHEPYYRYPEQMKVFAREVGATVQVAGGVP------AMCDGV 117
           DF +  I +  S+   +  H         +K   + V   ++ AGGV       A+ DG+
Sbjct: 31  DFGKPIIAIANSFTQFVPGHV-------HLKDLGQMVAREIEKAGGVAKEFDTIAIDDGI 83

Query: 118 TQGQPGMEESLFSRDVIALATSVSLSHGMFEGAALLGICDKIVPGLLMGALRFGHLPTIL 177
             G  GM  SL SR++IA +    ++    +    +  CDKI PG+LM +LR  ++PTI 
Sbjct: 84  AMGHAGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRL-NIPTIF 142

Query: 178 VPSGPMTTG--IPNKEKIRIRQLYAQGKIGQKELLDMEAACYHAE-----GTCTFYGTAN 230
           +  GPM  G      E   +  + A  K   + + D EA  +  E     G+C+   TAN
Sbjct: 143 ISGGPMEAGKVTYQGETHAVDLIDAMIKGADQNVSDEEALAFEKESCPTCGSCSGMFTAN 202

Query: 231 TNQMVMEVLGLHMPGSAFVTPGTPLRQALTRAAVHRVAELG---WKGDDYRPLGKIIDE- 286
           +   ++E LGL +PG+  V      R+ L   A  R+ +L    ++GDD   L + I   
Sbjct: 203 SMNCLIEALGLGLPGNGTVVATHADRKELFLEAGRRIVDLARRAYEGDDASVLPRSIATF 262

Query: 287 KSIVNAIVGLLATGGSTNHTMHIPAIARAAGVIVNWNDFHDLSEVVPLIARIYPNGPR-D 345
           ++  NA+   +A GGSTN  +H+ A A+ AGV    +D   LS  VP + ++ PN P   
Sbjct: 263 QAFENAMTLDIAMGGSTNTVLHLLAAAQEAGVAFGMSDIDRLSRRVPCLCKVAPNVPDVH 322

Query: 346 INEFQNAGGMAYVIKELLSANLLNRD-----VTTIAKG-------------GIEEYAKAP 387
           I +   AGG+  ++ +L    L+NR+       T+A+G              +E Y  AP
Sbjct: 323 IEDVHRAGGIMGILGQLDRGGLINRECGTIHARTLAEGLDRWDISRSNDPKVVEFYKAAP 382

Query: 388 ALNDAGELV-----WKPAGEPGDDTILRPVSNPFAKDGGLRLLEGNLG--RAMYKASAVD 440
                 E       W    +     ++R V N F+KDGGL +L GNL     + K + VD
Sbjct: 383 GGVRTTEAFSQSKRWAEVDKDRTAGVIRSVDNAFSKDGGLAVLFGNLALDGCIVKTAGVD 442

Query: 441 PKFWTIEAPVRVFSDQDDVQKAFKAGELNKDVIVVVRFQGPRAN-GMPELHKLTPALGVL 499
            K  T   P  +   QD+       G++    +V+VR++GPR   GM E+   T  L  +
Sbjct: 443 DKNLTFSGPAVICESQDEAVAKILGGQVKSGDVVIVRYEGPRGGPGMQEMLYPTSYLKSM 502

Query: 500 QDNGYKVALVTDGRMSGATGKVPVALHVSPEALGGGAIGKLRDGDIVRISVEEGKLEALV 559
              G + AL+TDGR SG T  + +  HVSPEA  GGAIG ++ GDI+ I +    +   V
Sbjct: 503 -GLGKECALITDGRFSGGTSGLSIG-HVSPEAAEGGAIGLIQAGDIIDIHIPNRSIAIRV 560

Query: 560 PADEWNAR--------PHAEKPAFRPGTGRELFDIFRQNAAKAEDGAV 599
              E   R        P A KP  R          +      A  GAV
Sbjct: 561 SDAELEKRRQAMQALGPKAWKPVDRDRQVSAALRAYAAMTTSAARGAV 608


Lambda     K      H
   0.318    0.136    0.403 

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: 988
Number of extensions: 53
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: 607
Length of database: 616
Length adjustment: 37
Effective length of query: 570
Effective length of database: 579
Effective search space:   330030
Effective search space used:   330030
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

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

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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