GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolA in Pseudomonas fluorescens FW300-N1B4

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate Pf1N1B4_1109 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= metacyc::MONOMER-15203
         (503 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1109 2-ketoglutaric
           semialdehyde dehydrogenase (EC 1.2.1.26)
          Length = 481

 Score =  276 bits (706), Expect = 1e-78
 Identities = 173/480 (36%), Positives = 249/480 (51%), Gaps = 9/480 (1%)

Query: 4   KRIEHYINGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWSDTP 63
           KR ++YING   +G AD    +         G  A A  A V +A+ AA+AAFPAWS + 
Sbjct: 5   KRYDNYINGEWVSG-ADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSG 63

Query: 64  PIRRARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLLKG 123
              R   + K    + A ++EL   + RE GK   +A GEV R  +I +F  G    L G
Sbjct: 64  IQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSG 123

Query: 124 DYTEQVSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSA 183
           DY   V  G++   TR+ LGVV  ITP+NFP+ +P W    A+A GN  VLKP+ L P  
Sbjct: 124 DYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGC 183

Query: 184 SLMMADLLKQAGLPDGVFNVVQGDKDSV-EALIDHPDVKALSFVGSTPIANLIYERGARS 242
           +  +A+++ +AG P GVFN+V G    V +AL+  P V  +SF GS  +   I       
Sbjct: 184 AWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVSR 243

Query: 243 GKRIQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPR 302
             ++Q   G KN  +++ DA+L +AV+  + +A+ S G+RC A S  ++   + DK V  
Sbjct: 244 QAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEA 303

Query: 303 LAERARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGE 362
           +AER + +K+ + L+   ++GP+V+    ++   YI+ G +EGA +V  G          
Sbjct: 304 MAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACD---- 359

Query: 363 GCADGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFT 422
              +G+++  TLF   T  M I REEIFGPV   VRV D   A+ + ND EFG      T
Sbjct: 360 --TEGYFLAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIAT 417

Query: 423 ESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQKS 482
            S   A  F R  Q GMV +N+P         FGG K S +G +   G     FYT  K+
Sbjct: 418 TSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYG-SREQGRYAQEFYTVVKT 476


Lambda     K      H
   0.319    0.136    0.406 

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: 577
Number of extensions: 28
Number of successful extensions: 4
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: 503
Length of database: 481
Length adjustment: 34
Effective length of query: 469
Effective length of database: 447
Effective search space:   209643
Effective search space used:   209643
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: 52 (24.6 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 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