GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Sphingomonas koreensis DSMZ 15582

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Ga0059261_1495 Ga0059261_1495 succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)

Query= BRENDA::P76217
         (492 letters)



>FitnessBrowser__Korea:Ga0059261_1495
          Length = 480

 Score =  432 bits (1112), Expect = e-125
 Identities = 228/460 (49%), Positives = 298/460 (64%), Gaps = 5/460 (1%)

Query: 14  GASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAVVERFAALLE 73
           G+  +   P +G VLW+    D   V+    AARA++  WA      R   + RFA ++ 
Sbjct: 12  GSEIISTEPATGAVLWRRPIGD---VDAEVAAARASWADWAARPLTYRIEALRRFANVVR 68

Query: 74  SNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEMP-DGAASLRH 132
                 T +IARETGKP WEA TEV  +I K+ IS+ A+  RTG++R E P +   +LRH
Sbjct: 69  QKSEAFTDLIARETGKPLWEARTEVETVIAKVDISVTAFSERTGQRRIEAPMNTRLALRH 128

Query: 133 RPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRLWQQAGLPPG 192
           +PHGVLAV GPYNFP HLPNGHIVPALLAGN ++FKPSE TP +G  ++  +  AG+P G
Sbjct: 129 KPHGVLAVLGPYNFPAHLPNGHIVPALLAGNAVVFKPSEKTPATGAFLVECYHAAGIPEG 188

Query: 193 VLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALEMGGNNPLII 252
            + L+ GG + G+AL+  + +DGLLFTGSA TG  L+R  + +PEKILALEMGGNNP+++
Sbjct: 189 CIRLLIGGPDEGKALAGHDGIDGLLFTGSARTGIALNRAFAAKPEKILALEMGGNNPILV 248

Query: 253 DEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQRLTPGNWDD 312
               DI +A  L IQSAF +AGQRCT ARRL++      D  L  +  +  RL  G    
Sbjct: 249 WSTPDIYSAAVLVIQSAFTSAGQRCTAARRLIVDEKLY-DPLLEEVNKLIGRLIVGEPHA 307

Query: 313 EPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGIIEMTGVAGVP 372
           +P PF+G +I    A  +  ++ +L  MGGRPL        G   LTP +I+MT     P
Sbjct: 308 DPAPFMGPVIDNDTADLLTESFLELSFMGGRPLRHMERPVDGRPFLTPAMIDMTDAKEKP 367

Query: 373 DEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEARAGIVNWNKP 432
           D E+FGP+L+V R  TF+EAI  ANNTR+GLS  LVS + + +DQ     RAGIVNWN+P
Sbjct: 368 DVELFGPILQVIRARTFEEAIAEANNTRYGLSASLVSQDPKLYDQFWANIRAGIVNWNRP 427

Query: 433 LTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESD 472
             GA+S APFGGIG SGNHRPSA+YAADYCA+P+ S E++
Sbjct: 428 TNGASSAAPFGGIGWSGNHRPSAFYAADYCAYPVVSSEAE 467


Lambda     K      H
   0.318    0.134    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: 691
Number of extensions: 38
Number of successful extensions: 3
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: 492
Length of database: 480
Length adjustment: 34
Effective length of query: 458
Effective length of database: 446
Effective search space:   204268
Effective search space used:   204268
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 (21.7 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