GapMind for catabolism of small carbon sources

 

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

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_011385957.1 AMB_RS18215 acyl-CoA dehydrogenase

Query= BRENDA::Q18AQ1
         (378 letters)



>NCBI__GCF_000009985.1:WP_011385957.1
          Length = 378

 Score =  357 bits (916), Expect = e-103
 Identities = 178/372 (47%), Positives = 248/372 (66%)

Query: 5   SKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGD 64
           +++ Q+++++  SFA  ++ P A   D E  FP + + +M + G +G+  P E+ G G D
Sbjct: 4   TEEQQLIRDMARSFAREKLAPNAARWDREHLFPTDAIAEMGELGFLGMVVPSEWDGAGTD 63

Query: 65  TVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGL 124
            V Y MAV E++  CG    I+S H S+G  PI  YG E QK +FLRP+A GEKLG F L
Sbjct: 64  YVSYAMAVMEIAAGCGPLSTIMSVHNSVGCMPILTYGTEAQKDEFLRPMARGEKLGCFCL 123

Query: 125 TEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFI 184
           TEP AG+DA+  +T A  DGD Y+L+G+K FI+ A  G + +V A+TD   G +GISAF+
Sbjct: 124 TEPEAGSDAASIRTRARRDGDHYVLSGAKQFISTAKNGQVAIVFAVTDPQAGKRGISAFV 183

Query: 185 VEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIG 244
           V   TPGF+    E K+G   S T +L FED R+P    LG+EG G KIA++ L+GGR+G
Sbjct: 184 VPTDTPGFTVVRVEDKLGQHLSDTCQLAFEDMRVPASRRLGEEGDGLKIALANLEGGRLG 243

Query: 245 IAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAIN 304
           IAAQ++G+A+ ALD  + Y KER QFG+P+ + Q   F+LADM  +V+ A  +V  AA  
Sbjct: 244 IAAQSVGMARSALDHALAYAKERKQFGKPIFEHQAVAFRLADMATRVEVAEQMVLHAASL 303

Query: 305 KDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGT 364
           +D G P   EA+MAKLFA+E A  V + A+Q+HGGYGY  D+PVER+ RD ++ +IYEGT
Sbjct: 304 RDAGLPCLKEASMAKLFASEMAERVCSDAIQIHGGYGYLADFPVERIYRDVRVCQIYEGT 363

Query: 365 SEVQRMVISGKL 376
           S++QR+VIS  L
Sbjct: 364 SDIQRLVISRAL 375


Lambda     K      H
   0.315    0.133    0.373 

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: 347
Number of extensions: 10
Number of successful extensions: 1
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: 378
Length of database: 378
Length adjustment: 30
Effective length of query: 348
Effective length of database: 348
Effective search space:   121104
Effective search space used:   121104
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: 42 (22.0 bits)
S2: 50 (23.9 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