GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Magnetospirillum magneticum AMB-1

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_011382620.1 AMB_RS00880 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase

Query= BRENDA::P77455
         (681 letters)



>NCBI__GCF_000009985.1:WP_011382620.1
          Length = 515

 Score =  466 bits (1199), Expect = e-135
 Identities = 248/512 (48%), Positives = 329/512 (64%), Gaps = 5/512 (0%)

Query: 1   MQQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMT 60
           M +L S+L+G WQ G G    +   +SGE L   + +GLD+A A  FA ++G PALRA++
Sbjct: 1   MIRLQSYLAGRWQDGAGSGAQLKDPVSGEVLATASGDGLDIAEALAFARDRGGPALRALS 60

Query: 61  FIERAAMLKAVAKHLLSEKERFYALS-AQTGATRADSWVDIEGGIGTLFTYASLGSRELP 119
           F  RA ++ A+A  L   +ER+  ++ A +G T  D+ +D++GGIGTL  YAS+G R+L 
Sbjct: 61  FAGRAGLINALAGVLAENRERYNTVALANSGNTAVDAGLDVDGGIGTLKYYASIG-RKLG 119

Query: 120 DDTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAI 179
           +  L  E     L+K+  F  RH+ TS  GVAVHINAFNFP WG+ EK A + L G+P +
Sbjct: 120 EARLLAEATDDQLTKDEAFRGRHIWTSNRGVAVHINAFNFPSWGLWEKAAVSLLAGVPFL 179

Query: 180 IKPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQM 239
            KPATAT+ L   MVK +V +G++PEGA+SL+CG   DL+DHL   DVV FTGSA T   
Sbjct: 180 AKPATATSWLAYEMVKDVVAAGVLPEGAMSLLCGGGRDLMDHLKPGDVVAFTGSAETAAQ 239

Query: 240 LRVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIR 299
           LR  PN++A ++ F +EADSLN C LG D  PD PEFA FI+EV REMT KAGQKCTAIR
Sbjct: 240 LRSNPNVIAANVRFAVEADSLNLCALGPDAAPDAPEFAAFIKEVSREMTVKAGQKCTAIR 299

Query: 300 RIIVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCE 359
           R++VP++ V+ V  AL   L K ++GDP  EGV+MG LV+  Q       +  L A    
Sbjct: 300 RVLVPRSRVDDVVAALKPALAKALMGDPRTEGVRMGPLVSRAQTVAAWAGLEALKAETQV 359

Query: 360 IRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACAG 419
           +  GG  D    G F P TLL C  P    AVH  E FGPVATLMP  +   A+ LA  G
Sbjct: 360 VAGGGNDD---GGCFVPATLLLCNDPLAARAVHEIEVFGPVATLMPYDSVEQAVDLAHKG 416

Query: 420 GGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRAG 479
           GGSLA ++ + D      F+   A +HGR+ +++   A   +GHG  +P  +HGGPGRAG
Sbjct: 417 GGSLAASVFSGDAAFLAGFVPAIATSHGRVLVVDSSVAASHSGHGVVMPHCIHGGPGRAG 476

Query: 480 GGEELGGLRAVKHYMQRTAVQGSPTMLAAISK 511
           GGEELGGLR ++ YMQR+A+QGS +ML A+++
Sbjct: 477 GGEELGGLRGLRFYMQRSAIQGSRSMLDAMTQ 508


Lambda     K      H
   0.319    0.134    0.395 

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: 843
Number of extensions: 35
Number of successful extensions: 4
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: 681
Length of database: 515
Length adjustment: 37
Effective length of query: 644
Effective length of database: 478
Effective search space:   307832
Effective search space used:   307832
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: 53 (25.0 bits)

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

Links

Downloads

Related tools

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