GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011383248.1
          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:

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