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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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