GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Pseudomonas putida KT2440

Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate PP_0545 PP_0545 aldehyde dehydrogenase

Query= metacyc::MONOMER-13349
         (490 letters)



>FitnessBrowser__Putida:PP_0545
          Length = 506

 Score =  350 bits (897), Expect = e-101
 Identities = 192/491 (39%), Positives = 291/491 (59%), Gaps = 17/491 (3%)

Query: 3   QYRNYINGEWVESARR--FDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTT 60
           +Y NYI GE+V   +   F++ +PV+G ++A+   +  E +D A+ A HAA   AWGRT+
Sbjct: 18  RYGNYIGGEFVTPVKGQYFENTSPVNGKLIAEFPRSTAEDIDKALDAAHAAA-DAWGRTS 76

Query: 61  VAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAP 120
           V +R+ +L +IAD I++  +     E  D GKP+      DIP    +FR FA  ++   
Sbjct: 77  VQDRSNVLLKIADRIEQNLELLAITETWDNGKPIRETLNADIPLAVDHFRYFAGCIRAQ- 135

Query: 121 LDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEE 180
            +    ++ +G  A  Y + +PLGVVG I PWN P+L+  WK+APALA GN VV KP+E+
Sbjct: 136 -EGGAAEINEGTVA--YHIHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQ 192

Query: 181 TPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMR 240
           TP   T+L EV+  + +PPGV N+V G+G + AGE + T+  I  I FTG +  GS IM+
Sbjct: 193 TPLGITVLLEVIGDL-LPPGVLNVVQGYGRE-AGEALATSKRIAKIAFTGSTPVGSHIMK 250

Query: 241 AAATHVKPVSFELGGKNAAIIFADCD------FEKMIDGMMRAVFLHSGQVCLCAERVYV 294
            AA ++ P + ELGGK+  + F D         EK  +GM+ A F + G+VC C  R  V
Sbjct: 251 CAAENIIPSTVELGGKSPNVYFEDIMQAEPSFIEKAAEGMVLA-FFNQGEVCTCPSRALV 309

Query: 295 ERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVG 354
           +  IY +F++  +++V  +K G P D  T +G   S +  +K+LSY ++A+EEGA++L G
Sbjct: 310 QESIYPQFMEVVMKKVLQIKRGDPLDTDTMVGAQASQQQFEKILSYLQIAQEEGAELLTG 369

Query: 355 GGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKY 414
           G V K   +   G++++PT++ G     R  +EE+FGP+  V+ F  EAEA+A+ANDT++
Sbjct: 370 GKVEKLEGSLATGYYIQPTLLKG-NNKMRVFQEEIFGPVVSVTTFKDEAEALAIANDTEF 428

Query: 415 GLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFY 474
           GL A  WT ++NR +R+   ++ G  W N + L      FGG   SG+GRE     L+ Y
Sbjct: 429 GLGAGVWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHY 488

Query: 475 SELTNVCVRID 485
            +  N+ V  D
Sbjct: 489 QQTKNLLVSYD 499


Lambda     K      H
   0.321    0.137    0.420 

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: 580
Number of extensions: 23
Number of successful extensions: 7
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: 490
Length of database: 506
Length adjustment: 34
Effective length of query: 456
Effective length of database: 472
Effective search space:   215232
Effective search space used:   215232
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.

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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