GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011385957.1
          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.

Links

Downloads

Related tools

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