GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Sphingomonas koreensis DSMZ 15582

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Ga0059261_0516 Ga0059261_0516 vanillin dehydrogenase (EC 1.2.1.67)

Query= BRENDA::G5DDC2
         (506 letters)



>FitnessBrowser__Korea:Ga0059261_0516
          Length = 478

 Score =  219 bits (558), Expect = 2e-61
 Identities = 165/484 (34%), Positives = 240/484 (49%), Gaps = 24/484 (4%)

Query: 21  PPAQGRRLPVVNPTTEAHIGEIPAGTAEDVDAAVAAARAALKRNRGRDWARAPGAVRAKY 80
           PPA G+    +NP T     E  A T +  + AV AA AA        W+      R   
Sbjct: 6   PPAPGKTFARLNPVTGEVATEAQAFTVDQANEAVEAAAAAFPA-----WSTLGPNARRAA 60

Query: 81  LRAIAAKVIERKQELAKLEALDCGKPYDEAAWDMDDVAGCFEYFADQAEALDKRQNSPVS 140
           L   A  +  + ++  +    + G     A +++            +A AL  +    V 
Sbjct: 61  LNKAAEALAAKAEDFVEAMNGEIGATEGWARFNLMLAVSMVR----EAAALTTQIGGEV- 115

Query: 141 LPMETFKCHLR--REPIGVVGLITPWNYPLLMATWKVAPALAAGCAAVLKPSELASVTCL 198
           +P +   C     REP+GV+  I PWN P+++    VA  LA G   VLK SE    T  
Sbjct: 116 IPSDKPGCIAMAIREPVGVMLGIAPWNAPIILGVRAVAAPLACGNTVVLKASEQCPRTHS 175

Query: 199 ELADICKEVGLPPGVLNIVTGLGPDAGAPLSA---HPDVDKVAFTGSFETGKKIMAAAAP 255
            +A+   E  LP G ++IVT    DA   + A   +P + ++ FTGS   G+ I   AA 
Sbjct: 176 LIAEAFDEA-LPKGAVSIVTNAPEDAPEIVGALIDNPHIRRINFTGSTAVGRIIAKRAAE 234

Query: 256 MVKPVTLELGGKSPIVVFDDVDIDKAVEWTLFGCFWTNGQICSATSRLLVHTKIAKEFNE 315
            +KPV LELGGK+P++V +D D+D+AV+   FG F   GQIC +T R++V   +A  F E
Sbjct: 235 HLKPVLLELGGKAPMLVLEDADLDEAVKAAAFGAFMNQGQICMSTERIIVVDAVADAFVE 294

Query: 316 KMVAWAKNIKVSDPLEEGCRLGPVVSEGQYEKIKKFILNAKSEGATILTGGVRPAHLE-- 373
           K  A    + V DP E    LG VV +     +K  I +A + GA  + GG     LE  
Sbjct: 295 KFAAKVGTMPVGDPREGKTPLGAVVDQKTVAHVKALIGDALAAGAVQVNGG---GVLEGT 351

Query: 374 KGFFIEPTIITDITTSMEIWREEVFGPVLCVKEFSTEDEAIELANDTQYGLAGAVISGDR 433
            G  +   +I  +T  M+++R+E FGPV+ V     E  AI LANDT+YGL+ +V + D 
Sbjct: 352 GGVLMPAHVIDHVTPDMKLFRDESFGPVVGVIRARDEAHAILLANDTEYGLSASVFTRDT 411

Query: 434 ERCQRLSEEIDAGIIWVN-CSQPCFCQAPWGGNKRSGFGRELGEGGIDNYLSVKQVTEYI 492
            R  R++ +I +GI  VN  +     Q P+GG K SG+GR  G+ GID +  ++ +T  I
Sbjct: 412 ARGLRVARQIKSGICHVNGPTVHDEAQMPFGGVKASGYGRFGGKAGIDAFTELRWIT--I 469

Query: 493 SDEP 496
             EP
Sbjct: 470 ETEP 473


Lambda     K      H
   0.318    0.135    0.421 

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: 569
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: 506
Length of database: 478
Length adjustment: 34
Effective length of query: 472
Effective length of database: 444
Effective search space:   209568
Effective search space used:   209568
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.

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