GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Pseudomonas putida KT2440

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate PP_3646 PP_3646 Aldehyde dehydrogenase family protein

Query= reanno::pseudo5_N2C3_1:AO356_23175
         (500 letters)



>FitnessBrowser__Putida:PP_3646
          Length = 493

 Score =  244 bits (623), Expect = 5e-69
 Identities = 151/473 (31%), Positives = 252/473 (53%), Gaps = 8/473 (1%)

Query: 11  IDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFP--AWSEQSSLRR 68
           IDG+ + + + +  +  NPAT    A++  A+ + V+ AV +A  AF   AW   ++  R
Sbjct: 10  IDGQWRDAQSGKTFDSLNPATAQAWAQLPDADEADVELAVQAAQRAFDSKAWRSITATAR 69

Query: 69  SRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSD 128
            +++ +  +L+  + + LAQ+ SR++GK++ +  G+V    E   Y  G  + L+     
Sbjct: 70  GKLLRRLGDLIAENKEHLAQLESRDNGKLIRETRGQVGYLPEFFHYTAGLADKLEGGTLP 129

Query: 129 NIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLM 188
                +  + + +P+GV AG+ P+N P+ +    +  AL AGN  +LKPSE   +  L +
Sbjct: 130 LDKPDLFAYTVHEPIGVVAGIIPWNSPLYLTAIKLAPALAAGNTIVLKPSEHASATILEL 189

Query: 189 ARLLTEAGLPDGVFNVVQGDKVAVDALL-QHPDIEAISFVGSTPIAEYIHQQGTAQGKRV 247
           ARL  EAG P GV NVV G   +  A L +HP +  I+F G    A ++ +       ++
Sbjct: 190 ARLALEAGFPAGVVNVVTGYGPSTGAALTRHPLVRKIAFTGGAATARHVVRSSAENFAKL 249

Query: 248 QALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPR 307
               G K+  I+  DADLD A +  +   Y ++G+ C+A S  +   ++ DE + +L+ R
Sbjct: 250 SLELGGKSPNIIFADADLDSAINGAVAGIYAASGQSCVAGSRLLVQDEIFDEFVERLIAR 309

Query: 308 IDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFFV 367
             +++IGN Q   ++MGP+ TA+  A VEG + A  AEGA+L + G+   V G   G+F 
Sbjct: 310 AKRIRIGNPQDDASEMGPMATAQQLAVVEGLVAAAKAEGAKLHMGGKRADVEG--DGWFY 367

Query: 368 GATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARA 427
             TLF+  +  M+I Q+E+FGPV  ++R      A+A+ N  +FG     +TRD G A  
Sbjct: 368 EPTLFECDSNAMTIMQEEVFGPVAAVIRFKTEEEALAMANDSQFGLAAGIWTRDLGRAHR 427

Query: 428 FARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSV 480
            AR ++ G++ +N    V  A    GG+K S +G     G + +  Y+  K+V
Sbjct: 428 LARDVRSGIIWVNTYRAV-SAMAPIGGFKNSGYG--RESGIDSVLAYTELKTV 477


Lambda     K      H
   0.320    0.137    0.412 

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: 547
Number of extensions: 30
Number of successful extensions: 5
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: 500
Length of database: 493
Length adjustment: 34
Effective length of query: 466
Effective length of database: 459
Effective search space:   213894
Effective search space used:   213894
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