GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etfA in Magnetospirillum magneticum AMB-1

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate WP_011386257.1 AMB_RS19755 electron transfer flavoprotein subunit alpha

Query= BRENDA::Q18AQ5
         (336 letters)



>NCBI__GCF_000009985.1:WP_011386257.1
          Length = 311

 Score =  172 bits (436), Expect = 1e-47
 Identities = 119/323 (36%), Positives = 179/323 (55%), Gaps = 16/323 (4%)

Query: 4   VLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHY-GADEVI 62
           +LV+ E     +++ +L  +  A++I  D    V  L+ GS +  + +  A   G  +V+
Sbjct: 3   ILVIAEHEGGALKSATLNTVSAASKIGGD----VHVLVAGSGIGAVAEAAAKVAGVAKVL 58

Query: 63  VVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTG 122
             D    A +  EP   AA     A     +L  AT+ G+++APRV+A +     ++ T 
Sbjct: 59  SADAALYANHLAEPL--AALVVSLAGSYSHILAPATTGGKNVAPRVAALLDVAQISEITA 116

Query: 123 LAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRFKV 182
           + V+ DT      RP + GN +AT+  KD   ++ TVR G   +    E   A +     
Sbjct: 117 V-VSPDT----FVRPIYAGNALATVQSKD-AVKVITVR-GTGFEAAKAEGGSASVEAVSA 169

Query: 183 EFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGEVSGS 242
             + A       Q+ K  + +  +  A+I++S GRGM   +N  +L  +A+ +G  V  S
Sbjct: 170 AADPALSSFVGSQLSKSERPE--LTSARIIISGGRGMQSGDNFHLLEAVADKLGAAVGAS 227

Query: 243 RATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAPIF 302
           RA +DAG++    QVGQTGK V PDLYIA GISGAIQH+AGM+D++ IVAINK+ EAPIF
Sbjct: 228 RAAVDAGFVPNDFQVGQTGKIVAPDLYIAVGISGAIQHLAGMKDSKVIVAINKDEEAPIF 287

Query: 303 KYADVGIVGDVHKVLPELISQLS 325
           + AD G+V D+ KVLPEL S+L+
Sbjct: 288 QVADYGLVADLFKVLPELASELN 310


Lambda     K      H
   0.316    0.135    0.371 

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: 269
Number of extensions: 15
Number of successful extensions: 2
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: 336
Length of database: 311
Length adjustment: 28
Effective length of query: 308
Effective length of database: 283
Effective search space:    87164
Effective search space used:    87164
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 (21.6 bits)
S2: 48 (23.1 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