GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Dinoroseobacter shibae DFL-12

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 3609638 Dshi_3021 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__Dino:3609638
          Length = 485

 Score =  301 bits (770), Expect = 4e-86
 Identities = 187/477 (39%), Positives = 268/477 (56%), Gaps = 17/477 (3%)

Query: 20  NRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSS 79
           + + I G +   A+  T E +DP    PLA+IARG + +IDRA++AAR   + GDW   S
Sbjct: 14  DEILIGGVWQRCAD--TLEVIDPSDGTPLAQIARGGAAEIDRAVAAARAALD-GDWGRMS 70

Query: 80  PAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVY 139
             +R   L +L  L+    + LA +E  D GKP+  + R D    AR + +Y  A DKV 
Sbjct: 71  ATERGRCLTRLGALVAGEVDRLAEMEARDVGKPLSQA-RADALALARYLEFYGGAADKVM 129

Query: 140 GEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLS 199
           GE     S      +REP GV   IVPWN+P+ +    +G ALA GN+ +LKP+E + L+
Sbjct: 130 GETIPYQSGYTVYTLREPHGVTGHIVPWNYPMQIIGRSVGAALAMGNACVLKPAEDACLT 189

Query: 200 AIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDS 259
           A+  A LA+ AGLP G LNVVTG G EAG ALS H  +D ++FTGS   G ++   A   
Sbjct: 190 ALAFARLAEAAGLPPGALNVVTGLGAEAGAALSDHPGVDHLSFTGSVPVGAEVQATAA-R 248

Query: 260 NMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFL 319
           ++  V LE GGKS  IVFAD  DL  A      G   N GQ C A  R+L++  + D   
Sbjct: 249 HITPVTLELGGKSPQIVFADA-DLDAALPFLVKGGVQNAGQTCSAAARILVQTDVFDAVA 307

Query: 320 ALLKQQAQNWQPGHPL-DPATTMGTLIDCAHADSVHSFIREGE-----SKGQLLLDGRNA 373
             + +  +    G  L DPA  +G LI       V + + + +     + G LL +    
Sbjct: 308 DRMAEAYRALTVGPALSDPA--VGPLISPKQKARVSAMLAQAQPDQILATGHLLPEAPEG 365

Query: 374 GLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRD 433
           G    + P +   +  +  L+++EIFGPV ++ RF +E++A+ LAN +++GL A +WTRD
Sbjct: 366 G--CYVLPHLLGGIAADHPLAQQEIFGPVQILMRFETEQEAIALANGTEFGLVAGIWTRD 423

Query: 434 LSRAHRMSRRLKAGSVFVNNYN-DGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489
            +R  RM +RL+AG VFVN Y   G + +PFGG  +SG+GR+K   AL  F++LKT+
Sbjct: 424 GARQMRMPKRLRAGQVFVNTYGAGGGVELPFGGVGKSGHGREKGFEALFGFSQLKTV 480


Lambda     K      H
   0.317    0.133    0.389 

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: 558
Number of extensions: 28
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: 495
Length of database: 485
Length adjustment: 34
Effective length of query: 461
Effective length of database: 451
Effective search space:   207911
Effective search space used:   207911
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