GapMind for catabolism of small carbon sources

 

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

Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= BRENDA::P49189
         (494 letters)



>lcl|NCBI__GCF_000009985.1:WP_011383248.1 AMB_RS04115
           5-carboxymethyl-2-hydroxymuconate semialdehyde
           dehydrogenase
          Length = 485

 Score =  336 bits (862), Expect = 9e-97
 Identities = 184/469 (39%), Positives = 276/469 (58%), Gaps = 8/469 (1%)

Query: 24  DASGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAARI 83
           +++ T     PA   VI      GE EV  AV  AK AF  W+     +R ++L +   +
Sbjct: 12  ESASTIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPASQRAKLLRKVGDL 71

Query: 84  IREREDEIATMECINNGKSIFEAR-LDIDISWQCLEYYAGLAASMAGEHIQLPGGSFGYT 142
           I +  DEIA +E ++ G+S +  + + +  +     ++A     + GE          YT
Sbjct: 72  INQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGETYPT-NDHLNYT 130

Query: 143 RREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAGVP 202
             +P+GV   I  WN PF  A+WK+AP LA GN  V K S  +P+SA  L ++  EAG+P
Sbjct: 131 LYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSADRLGQLILEAGIP 190

Query: 203 PGLFNVVQG-GAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKGIKPVTLELGGKSPL 261
            G+FN+V G G+A G+ L +HPDV  VSFTGS  TG +I++    G+K  ++ELGGKSP 
Sbjct: 191 AGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQSG--GLKKYSMELGGKSPN 248

Query: 262 IIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIGDPL 321
           IIF DCD   AV  A++A +   G+ C NGTR+ VQ  + D+F   + ++T+++ +GDPL
Sbjct: 249 IIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAALAERTRKVVVGDPL 308

Query: 322 LEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPED--PKLKDGYYMRPCVLT 379
            E T +GP+I R H ++V  ++++   +GA+V+ GG +  PE   P LK+G ++RP VL 
Sbjct: 309 DEATNVGPMITRDHWKKVTSYIELGISEGARVVAGG-LGTPEGLAPHLKNGNFVRPTVLA 367

Query: 380 NCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAELQ 439
           +  +     +EEIFGPV  ++ F  EAE L+ AN T++GLA+ V+T +  RA R+   ++
Sbjct: 368 DVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTENGARAIRMAEGIE 427

Query: 440 AGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMG 488
           AG  F+N+ NV  +  PFGG K SG GRE G  + E + ++K VCV  G
Sbjct: 428 AGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVKNVCVSKG 476


Lambda     K      H
   0.320    0.137    0.411 

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: 599
Number of extensions: 26
Number of successful extensions: 5
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: 494
Length of database: 485
Length adjustment: 34
Effective length of query: 460
Effective length of database: 451
Effective search space:   207460
Effective search space used:   207460
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: 52 (24.6 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 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