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

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|NCBI__GCF_000009985.1:WP_011382620.1 AMB_RS00880
           3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
          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.

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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 preprint 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