GapMind for catabolism of small carbon sources

 

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

Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= SwissProt::Q9H2A2
         (487 letters)



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

 Score =  378 bits (971), Expect = e-109
 Identities = 200/478 (41%), Positives = 291/478 (60%), Gaps = 6/478 (1%)

Query: 9   MLENFIDGKFLPCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQE 68
           M+++ I+G+ +  +S I + +P+  EV C++   G+ E+  AV AA+EAFP W+     +
Sbjct: 1   MIKHLINGRQVESASTIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPASQ 60

Query: 69  RSRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSEC 128
           R+++L +V DL+ Q ++E A+ ES D G++    + M +PR+  NF FFA +  H   E 
Sbjct: 61  RAKLLRKVGDLINQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGET 120

Query: 129 TQM-DHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTA 187
               DHL   +YT+  PVGV GLISPWN+P    TWK AP +A GNT + K SEL+ ++A
Sbjct: 121 YPTNDHL---NYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSA 177

Query: 188 WMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHC 247
             L +L+ +AG+P GV NIV G G  VGEALV HP+V  +SFTGS  T  RI Q      
Sbjct: 178 DRLGQLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQSGG--L 235

Query: 248 KKLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRF 307
           KK S+ELGGK+P IIF+D + +  + A + + + N GE C   +RI VQ  +Y  F+   
Sbjct: 236 KKYSMELGGKSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAAL 295

Query: 308 VEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARN 367
            E TRK  VG P D   ++G +I++ H +KV SY++  ++EGA++  G       L    
Sbjct: 296 AERTRKVVVGDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGLAPHL 355

Query: 368 QAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSN 427
           + G F+ PTV+ D+ +      EEIFGPV CV+ F  E E ++ AN   YGLA+ VW+ N
Sbjct: 356 KNGNFVRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTEN 415

Query: 428 VGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITV 485
             R  R+A+ +++GLV+ N   +R+L  PFGG+K SG GREG   SY+ F E+K + V
Sbjct: 416 GARAIRMAEGIEAGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVKNVCV 473


Lambda     K      H
   0.319    0.133    0.404 

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: 584
Number of extensions: 19
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: 487
Length of database: 485
Length adjustment: 34
Effective length of query: 453
Effective length of database: 451
Effective search space:   204303
Effective search space used:   204303
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.

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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