GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Erythrobacter gangjinensis K7-2

Align 2-aminomucoate semialdehyde dehydrogenase subunit (EC 1.2.1.32) (characterized)
to candidate WP_082115713.1 AAW01_RS11260 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= metacyc::MONOMER-13321
         (542 letters)



>NCBI__GCF_001010925.1:WP_082115713.1
          Length = 1202

 Score =  117 bits (293), Expect = 3e-30
 Identities = 90/264 (34%), Positives = 124/264 (46%), Gaps = 27/264 (10%)

Query: 29  LVAIVHEASRELVDEAVKSGHQALSGEWGRTTATQRVALLRRIADEMERRQGDFLAAEMA 88
           +V  V  A  E   E+VK   +A  G W  T+  +R   L + AD +E R  + L   M 
Sbjct: 606 VVGHVSWAHEEGALESVKRAAEAFPG-WSSTSVHERAECLEKAADLLEDRMENLLGLIMR 664

Query: 89  DTGKPHSMASSIDVPRGIANFRTFADILATAPVDSHRLDLADGAYALNYSARKPLGVVGV 148
           + GK          P  IA  R   D L      +   D  DGA AL        G V  
Sbjct: 665 EAGK--------SAPNAIAEVREAVDFLRYYAQQAR--DSLDGADAL--------GPVVC 706

Query: 149 ISPWNLPLLLMTWKVAPALACGNTVVVKPSEDTPGTATLLAEVMEAAGVPPGVFNLVHGF 208
           ISPWN PL +   +V+ ALA GNTV+ KP+E+TP  A     +M  AGVP  V  LV G 
Sbjct: 707 ISPWNFPLAIFVGEVSAALAAGNTVLAKPAEETPLIAAQAIGIMHEAGVPEDVVQLVPGD 766

Query: 209 GPNSAGEFISSHPDISAITFTGESRTGTTIMRAAAE----GVKPVSF--ELGGKNAAIIF 262
           G    G  +   PDI  +TFTG +     I R  AE    G  P+ F  E GG+NA ++ 
Sbjct: 767 G--RIGAALVGSPDICGVTFTGSTEVAKIIQRQLAERLLPGGSPLPFIAETGGQNAMVVD 824

Query: 263 ADCDFDKMLDTMMRALFLNSGQVC 286
           +    ++++  ++ + F ++GQ C
Sbjct: 825 SSALPEQVVRDVVASAFDSAGQRC 848


Lambda     K      H
   0.319    0.135    0.423 

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: 1113
Number of extensions: 60
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: 542
Length of database: 1202
Length adjustment: 41
Effective length of query: 501
Effective length of database: 1161
Effective search space:   581661
Effective search space used:   581661
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 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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