GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Pseudomonas fluorescens GW456-L13

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate PfGW456L13_3737 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= BRENDA::Q88RC0
         (480 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3737
          Length = 496

 Score =  351 bits (900), Expect = e-101
 Identities = 191/480 (39%), Positives = 284/480 (59%), Gaps = 11/480 (2%)

Query: 10  RQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPA--WRAL 67
           R   +I+G+W+ A+ G +I V NPATG+ +            RA++++ KA  +  W +L
Sbjct: 17  RHGCFIDGQWVLAE-GDSIAVVNPATGQTLCETLDAPLELVERAVQSSHKAFKSGVWSSL 75

Query: 68  TAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKG-EIAYAASFIEWFAEEAKRI 126
              +R   L  +  L+ E+ ++LA+L T  QGK +  A+  ++     F+ + +  A +I
Sbjct: 76  RPADRERILLNFTRLVEEHAEELAQLETLSQGKSINMARALDLNATVEFMRYMSGWATKI 135

Query: 127 YGDTIPGHQP-----DKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKP 181
            G T     P            ++P+GV   I PWNFP  +   K  PALA GCT+++KP
Sbjct: 136 EGQTFDVSIPLPPGAKFTAFTKREPVGVVVGIVPWNFPLLIAAWKLMPALATGCTVIIKP 195

Query: 182 ASQTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQL 241
           A +TP +A+ L ELA  AGIPAGV +VVTG    VGG LT + LV K+SFTGST +G+ +
Sbjct: 196 AMETPLTAMRLAELALEAGIPAGVFNVVTGGGASVGGVLTQHPLVSKVSFTGSTAVGKSV 255

Query: 242 MEECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGV 301
              C +++ + SLELGG  P IV  DAD++KAV+GAI+    NNGQ C  A+R YV   +
Sbjct: 256 GVACMENMTRFSLELGGKNPMIVLADADIEKAVQGAILGGLLNNGQVCAAASRFYVHRSI 315

Query: 302 YDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLI 361
           +D F E LAAAV+ + IG G+       PL+  K    V +HIE A  +GA+V++GG+L+
Sbjct: 316 HDQFVEALAAAVSSMPIGAGMNCDAAINPLVSRKQQQSVLKHIELARQQGARVVTGGELL 375

Query: 362 EGN--FFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYAR 419
           EG+  F +PTIL D+  + AVA+EE FGP+  +  F DE  VI ++ND  +GLA+  +  
Sbjct: 376 EGDGFFVQPTILADIDHSMAVAREEVFGPVLGVMPFDDEDAVIELANDNRYGLAASLWTN 435

Query: 420 DMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCIS 479
           D+ +   +   +E G V +N  ++ +   PFGG+K SG+GRE  +  IE Y E+K +CI+
Sbjct: 436 DLGKAMNLVPRIEAGTVWVNAHVLLDPAMPFGGVKQSGMGREFGRAVIEAYTELKSVCIA 495


Lambda     K      H
   0.317    0.134    0.384 

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: 561
Number of extensions: 29
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: 480
Length of database: 496
Length adjustment: 34
Effective length of query: 446
Effective length of database: 462
Effective search space:   206052
Effective search space used:   206052
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 (21.6 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 (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