GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Pseudomonas putida KT2440

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate PP_5063 PP_5063 betaine aldehyde dehydrogenase, NAD-dependent

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__Putida:PP_5063
          Length = 490

 Score =  265 bits (677), Expect = 3e-75
 Identities = 167/483 (34%), Positives = 258/483 (53%), Gaps = 10/483 (2%)

Query: 1   MAEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTW 60
           MA     K YI+G +V++ +D   + +NPAT EVL  V  +T+ D++ A ++A    K W
Sbjct: 1   MARFGTQKLYIDGAYVDAGSDATFEAINPATGEVLAHVQRATEADVEKAVESAERGQKVW 60

Query: 61  SKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEA-LGEVGRGIENVEFAAGAP 119
           + +   +R+RIL     +L +  +ELA L T++ GK+  E    ++  G + +E+ AG  
Sbjct: 61  AAMTAMQRSRILRRAVDILRERNDELAMLETLDTGKSYSETRYVDIVTGADVLEYYAGLV 120

Query: 120 SLMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSE 179
             + G+ +  +         R P+GV  GI  +N+P+ +  W    A+A GN  I KPSE
Sbjct: 121 PAIEGEQIP-LRESSFVYTRREPLGVTVGIGAWNYPIQIALWKSAPALAAGNAMIFKPSE 179

Query: 180 RTPLLTEKLVELFEKAGLPKGVFNVVYGA-HDVVNGILEHPEIKAISFVGSKPVGEYVY- 237
            T L T KL E++ +AGLP GVFNV+ G+  +V   + EHP I+ +SF G    G+ V  
Sbjct: 180 VTSLTTLKLAEIYTEAGLPNGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTTTGKKVMA 239

Query: 238 KKGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIA 297
              S +LK V    G K+  I+  DA+L+      + A F S+G+ C     V +   + 
Sbjct: 240 SASSSSLKEVTMELGGKSPLIICADADLDKAADIAMMANFYSSGQVCTNGTRVFIPAEMK 299

Query: 298 DEFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENV 357
             F AK+ E+VA I++GN  D+    GP++   + +  L YI KG EEGAR++C G    
Sbjct: 300 AAFEAKIAERVARIRVGNPEDENTNFGPLVSFQHMESVLGYIAKGKEEGARVLCGGERLT 359

Query: 358 SDD---GYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACL 414
           + D   G FV PT+F + T +MTI K+EIF PV+S++  +  +E I  AN +++   A +
Sbjct: 360 AGDFAKGAFVAPTVFTDCTDDMTIVKEEIFGPVMSILTYETEEEVIRRANDTDYGLAAGV 419

Query: 415 FTSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRK 474
            T++          ++AG+  IN    +P A  P  G+K S  G    NG  S+  YTR 
Sbjct: 420 CTNDITRAHRIIHKLEAGICWINAWGESP-AEMPVGGYKQS--GVGRENGVSSLAQYTRI 476

Query: 475 KVV 477
           K V
Sbjct: 477 KSV 479


Lambda     K      H
   0.318    0.136    0.396 

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: 27
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: 487
Length of database: 490
Length adjustment: 34
Effective length of query: 453
Effective length of database: 456
Effective search space:   206568
Effective search space used:   206568
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