GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaH in Pseudomonas fluorescens GW456-L13

Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate PfGW456L13_2432 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-)

Query= reanno::Marino:GFF2749
         (506 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2432
           3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-)
          Length = 505

 Score =  585 bits (1508), Expect = e-171
 Identities = 295/505 (58%), Positives = 377/505 (74%), Gaps = 1/505 (0%)

Query: 1   MPALDTQTKVAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDK 60
           M AL+T  ++AV+GAGAMG+GIAQVAAQAGH V L D R GAA    +GI +QL +RV+ 
Sbjct: 1   MTALNTSARIAVIGAGAMGAGIAQVAAQAGHPVLLLDNRPGAAAQAIEGIDRQLGKRVEN 60

Query: 61  GKMQQQELDDVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILAT 120
           GK+  +     + R+  V  ++ +AD  L+IEAI+E+L++KR L   LE +C    ILA+
Sbjct: 61  GKLSAESRSATVARLQAVEVIETLADCDLIIEAIVENLEVKRALFRQLEGICGEHCILAS 120

Query: 121 NTSSISVTALGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGK 180
           NTSS+S+T++ A +  P+RL+G+HFFNPAP+MALVEVV GLA+   +A+ ++ TA AWGK
Sbjct: 121 NTSSLSITSIAAQLDHPQRLLGLHFFNPAPVMALVEVVSGLASDPALAECLYDTARAWGK 180

Query: 181 KPVYATSTPGFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIG 240
           KPV+  STPGFIVNRVARPFYAESLR+LQE A D  TLDA++REAG F MGAFELTDLIG
Sbjct: 181 KPVHTRSTPGFIVNRVARPFYAESLRMLQEGAADCPTLDALMREAGGFAMGAFELTDLIG 240

Query: 241 HDVNYAVTSSVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEP 300
           HDVNYAVT SVF++YYQD RFLPSLIQKELV+ GRLGRKSGQGFY Y + AE+PQ   E 
Sbjct: 241 HDVNYAVTCSVFDAYYQDTRFLPSLIQKELVDGGRLGRKSGQGFYCYAQGAERPQ-AGEI 299

Query: 301 AHQSDESVIIAEGNPGVAAPLLERLKAAGLTIIERDGPGQIRFGDAVLALTDGRMATERA 360
           +  +     IAEG+ G+A  LL RL   G+ +I RDG G +R GDAVLAL+DGRMA +RA
Sbjct: 300 SSSASVETCIAEGDLGIAQGLLARLSEQGVEVIRRDGRGLLRVGDAVLALSDGRMACQRA 359

Query: 361 ACEGVANLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADRPGLV 420
             +G+ NL+L DLAFDY  A R+A++ A      A+    ALLQ+AG+ VSL++D P L 
Sbjct: 360 REDGLRNLILLDLAFDYGNAKRIAISHAAGIDPLALEQGVALLQRAGLMVSLLSDSPALA 419

Query: 421 IMRTVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTNIQ 480
           ++RTVAMLANEAADA L GVA+ ADIDLAM+AG+NYP GPL+W+D +G  H+ + L N+Q
Sbjct: 420 VLRTVAMLANEAADALLQGVASAADIDLAMRAGVNYPQGPLAWADAIGLSHILETLENLQ 479

Query: 481 TSYAEDRYRPALLLRKNAFAQKGFY 505
            SY E+RYRP+LLLR+     + F+
Sbjct: 480 ASYGEERYRPSLLLRRRVAEGRTFH 504


Lambda     K      H
   0.318    0.133    0.375 

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: 689
Number of extensions: 27
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: 506
Length of database: 505
Length adjustment: 34
Effective length of query: 472
Effective length of database: 471
Effective search space:   222312
Effective search space used:   222312
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 (21.7 bits)
S2: 52 (24.6 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