GapMind for catabolism of small carbon sources

 

Aligments for a candidate for QDPR in Klebsiella michiganensis M5al

Align dihydromonapterin reductase (EC 1.5.1.50) (characterized)
to candidate BWI76_RS16230 BWI76_RS16230 dihydromonapterin reductase

Query= BRENDA::P0AFS3
         (240 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS16230 BWI76_RS16230
           dihydromonapterin reductase
          Length = 241

 Score =  374 bits (959), Expect = e-108
 Identities = 187/241 (77%), Positives = 209/241 (86%), Gaps = 1/241 (0%)

Query: 1   MGKTQPLPILITGGGRRIGLALAWHFINQKQPVIVSYRTHYPAIDGLINAGAQCIQADFS 60
           M   QP PILITGGGRRIGLALA HF+ ++QPVI+SYRT YPAID L  AGA C+ ADFS
Sbjct: 1   MADIQPRPILITGGGRRIGLALARHFVARQQPVIISYRTWYPAIDALREAGAVCLHADFS 60

Query: 61  TNDGVMAFADEV-LKSTHGLRAILHNASAWMAEKPGAPLADVLACMMQIHVNTPYLLNHA 119
           T++ ++AFA EV   ++ GLRAI+HNAS WMAEKPG PL  VLA MMQIHVN PYLLNHA
Sbjct: 61  TDESILAFAAEVEAHASGGLRAIIHNASGWMAEKPGIPLTTVLASMMQIHVNAPYLLNHA 120

Query: 120 LERLLRGHGHAASDIIHFTDYVVERGSDKHIAYAASKAALDNMTRSFARKLAPEVKVNSI 179
           LE LLRGHGHAASDIIH TDYVVERGSDKHIAYAASKAALDNM+RSFARKLAPE+KVN+I
Sbjct: 121 LESLLRGHGHAASDIIHITDYVVERGSDKHIAYAASKAALDNMSRSFARKLAPEIKVNAI 180

Query: 180 APSLILFNEHDDAEYRQQALNKSLMKTAPGEKEVIDLVDYLLTSCFVTGRSFPLDGGRHL 239
           APSLILFNE DDAEYR+QAL+KSLMK APGEKE+IDL +YL +S +VTGRSF +DGGRHL
Sbjct: 181 APSLILFNEGDDAEYRRQALDKSLMKIAPGEKEIIDLTEYLFSSSYVTGRSFAVDGGRHL 240

Query: 240 R 240
           R
Sbjct: 241 R 241


Lambda     K      H
   0.322    0.136    0.407 

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: 266
Number of extensions: 4
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: 240
Length of database: 241
Length adjustment: 23
Effective length of query: 217
Effective length of database: 218
Effective search space:    47306
Effective search space used:    47306
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 (21.9 bits)
S2: 46 (22.3 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, the preprint 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