GapMind for catabolism of small carbon sources

 

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

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_011385957.1 AMB_RS18215 acyl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385957.1 AMB_RS18215 acyl-CoA
           dehydrogenase
          Length = 378

 Score =  205 bits (522), Expect = 2e-57
 Identities = 124/370 (33%), Positives = 195/370 (52%), Gaps = 2/370 (0%)

Query: 20  DDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDY 79
           ++++++RD A ++A+ KLAP      R          EMGE+G LG  +P ++ G G DY
Sbjct: 5   EEQQLIRDMARSFAREKLAPNAARWDREHLFPTDAIAEMGELGFLGMVVPSEWDGAGTDY 64

Query: 80  VSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLT 139
           VSY +   E+        ++MSV +S+  +PI  +G++AQK+++L  +A GE +GCF LT
Sbjct: 65  VSYAMAVMEIAAGCGPLSTIMSVHNSVGCMPILTYGTEAQKDEFLRPMARGEKLGCFCLT 124

Query: 140 EPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD-EDGRDEIRGFIL 198
           EP  GSD  S+ TRAR+    Y LSG+K +I+ +    V +V+A  D + G+  I  F++
Sbjct: 125 EPEAGSDAASIRTRARRDGDHYVLSGAKQFISTAKNGQVAIVFAVTDPQAGKRGISAFVV 184

Query: 199 EKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENIL-PHVKGLRGPFTCLNSARYGI 257
                G +   +  K+G   S T ++  ++  VP    L     GL+     L   R GI
Sbjct: 185 PTDTPGFTVVRVEDKLGQHLSDTCQLAFEDMRVPASRRLGEEGDGLKIALANLEGGRLGI 244

Query: 258 AWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMK 317
           A  ++G A S    A  Y  +RKQFG+P+  +Q +  +LADM T + +  Q VL    ++
Sbjct: 245 AAQSVGMARSALDHALAYAKERKQFGKPIFEHQAVAFRLADMATRVEVAEQMVLHAASLR 304

Query: 318 DEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYEGTH 377
           D G   ++  S+ K  +   A  +   A  + GG G   +F V R   ++ V   YEGT 
Sbjct: 305 DAGLPCLKEASMAKLFASEMAERVCSDAIQIHGGYGYLADFPVERIYRDVRVCQIYEGTS 364

Query: 378 DIHALILGRA 387
           DI  L++ RA
Sbjct: 365 DIQRLVISRA 374


Lambda     K      H
   0.320    0.138    0.414 

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: 322
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: 395
Length of database: 378
Length adjustment: 30
Effective length of query: 365
Effective length of database: 348
Effective search space:   127020
Effective search space used:   127020
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: 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 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