GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etfA in Dyella japonica UNC79MFTsu3.2

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate N515DRAFT_4319 N515DRAFT_4319 electron transfer flavoprotein alpha subunit apoprotein

Query= BRENDA::Q18AQ5
         (336 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_4319 N515DRAFT_4319 electron
           transfer flavoprotein alpha subunit apoprotein
          Length = 314

 Score =  161 bits (407), Expect = 2e-44
 Identities = 105/329 (31%), Positives = 169/329 (51%), Gaps = 29/329 (8%)

Query: 1   MGNVLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHY-GAD 59
           M  +LVV E     + + +   +  A  +  D    +  L+L   V+ +    A   G  
Sbjct: 1   MSKILVVAEHLNGKLNSSTARAVSAAAAVKGD---SIDVLVLADSVDAIAAEAAKIDGVG 57

Query: 60  EVIVV----DDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTG 115
           +V+ +    +   LA        KAA      A    V F +T+ G+D+APRV+A +   
Sbjct: 58  KVLTIARAENAHPLAAVLAPQVAKAA------AGYSHVFFPSTTFGKDVAPRVAALLGVS 111

Query: 116 LTADCTGLAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVR----PGVMKKNEPDE 171
             +D   +  A   K     RP + GN + T+        ++T+R    P    + +   
Sbjct: 112 QVSDVMSVEGAHSFK-----RPIYAGNAIVTVEANPAHAVVATIRTASWPAAGSRGDSAA 166

Query: 172 TKEAVINRFKVEFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYEL 231
            +   ++             + V++ +    +  ++ A  +VS GRG+G KEN +++Y+L
Sbjct: 167 VEALAVDAALPAHT------RFVELQQGKSDRPDLQGAGKVVSGGRGVGSKENFEVIYKL 220

Query: 232 AEIIGGEVSGSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIV 291
           A+ IG  V  SRA +DAG++    QVGQTGK + P+LY+A GISGAIQH+ G++DA  IV
Sbjct: 221 ADKIGAAVGASRAAVDAGYVPNELQVGQTGKIIAPELYMAFGISGAIQHLTGIKDAGTIV 280

Query: 292 AINKNPEAPIFKYADVGIVGDVHKVLPEL 320
           AINK+ EAPIF+ AD+G+VGD+ K++PE+
Sbjct: 281 AINKDGEAPIFEIADIGLVGDLFKLIPEI 309


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: 254
Number of extensions: 12
Number of successful extensions: 3
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: 314
Length adjustment: 28
Effective length of query: 308
Effective length of database: 286
Effective search space:    88088
Effective search space used:    88088
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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