GapMind for catabolism of small carbon sources

 

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

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein

Query= BRENDA::Q402C7
         (499 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385953.1 AMB_RS18195 DUF1487
           domain-containing protein
          Length = 496

 Score =  375 bits (962), Expect = e-108
 Identities = 201/477 (42%), Positives = 291/477 (61%), Gaps = 6/477 (1%)

Query: 20  HFIGGEWVSGDSGKTIDLINPATGAVLTKIQAGNAKDIQRAVAAAKAAFPKWSESSPAER 79
           H IGG+ V    G+  ++ NPATG ++     G  +D+  AV +AKAA   W++ S   R
Sbjct: 20  HLIGGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIAVISAKAAQKDWAKQSARAR 79

Query: 80  QEILIEVARRLKARHQHYATLETLNNGKPIRESMYFDMPQAISQFEVFAGAAYGLHGQTL 139
            +++ E  R L A  +    L  L  GK +R     +       F  F G    L G+T+
Sbjct: 80  GKLVAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVLADMFTFFGGLGSELKGETI 139

Query: 140 DY-PDAIGIVHREPLGVCAQIIPWNVPILMMACKIAPALASGNTVVLKPAETVCLSVIEF 198
            + PD + +  REP+GV   IIPWNVP+L+MA K A AL +GN+VV+K AE   L+V+  
Sbjct: 140 PFNPDMLTVTVREPVGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEAPLTVLRV 199

Query: 199 FVEMADLLPPGVINVVTGYGADVGEALVTHEDVRKVAFTGSVATARRIIQYASSNIIPQT 258
              M  +LPPG+ N+++G+G + G  LV H DV+KV FTGSV T R + + A+  +IP T
Sbjct: 200 AEIMNTVLPPGLFNMLSGFGPECGAPLVEHPDVKKVTFTGSVETGRIVYKAAAEKLIPVT 259

Query: 259 LELGGKSAHIVCADADIDAAVESATMSTVFNK-GEVCLAGSRLFLHQSIQDEFLAKFKVA 317
           LELGGKS  IVCADAD+D AV  A     F + G+ C A SRLF+H+SI DEF+AK K  
Sbjct: 260 LELGGKSPMIVCADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHESIHDEFVAKVKAK 319

Query: 318 LEGIRQGDPLDFATQLGAQASQMQMDKVQSYLQLATE-EGAT--VLTGGSRNESLADGHF 374
           ++ +  GDPLD  T +G   S  Q+++V+SY+++  E +GAT  V +    +  LA G F
Sbjct: 320 VDAMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSALPTDPKLAKGRF 379

Query: 375 IKPTVFTNVSNSMRIAREEIFGPVTSVLTWNDEDDMMALANDTTYGLAGGVWTRDISRAH 434
           ++P +FT + NS R+ +EEIFGPV +V+ W+D +D++A AND+ YGLA  +WTRD   A 
Sbjct: 380 VQPVIFTGMKNSDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASIWTRDFKLAM 439

Query: 435 RIARKLETGTVWVNRYYNLKPNMPLGGYKQSGFGREFSHE-VLHHYTQTKSVVINLQ 490
              ++LE G V VN+   ++P +  GG K SG G+E S E +L H+T  K+++ N++
Sbjct: 440 DATKRLEAGFVQVNQNLVVQPGLSYGGVKTSGIGKEASLESMLEHFTHKKTIIFNMK 496


Lambda     K      H
   0.318    0.133    0.390 

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: 518
Number of extensions: 15
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: 499
Length of database: 496
Length adjustment: 34
Effective length of query: 465
Effective length of database: 462
Effective search space:   214830
Effective search space used:   214830
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 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