GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2432
          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:

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