GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011385953.1
          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 (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