GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Sulfuritalea hydrogenivorans sk43H DSM 22779

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_000828635.1:WP_041097806.1
          Length = 479

 Score =  309 bits (792), Expect = 1e-88
 Identities = 179/476 (37%), Positives = 269/476 (56%), Gaps = 17/476 (3%)

Query: 21  RLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSP 80
           + +I+G++ + A   T E   P   A LA + +G + D D+A++AARG F+   WS++  
Sbjct: 6   QFYIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDA--WSVTPA 63

Query: 81  AKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYG 140
           A+R A L K+ + ++A A+E+A   TL+ G P + S R  +     +   Y++ +     
Sbjct: 64  AERAAYLKKIQESLKARADEIAKTITLEMGMPYKFSQRIQVGSPTASFGMYSKMLADFPF 123

Query: 141 EVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSA 200
           E    +S     +VRE VGV+AAI PWN+PL     K+  ALAAG +V+LKPSE +PL+A
Sbjct: 124 EEKVGNSK----VVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPLNA 179

Query: 201 IRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSN 260
             LA +   AG+P GV N++TG+G   G+A+  H ++D ++FTGSTR G + + +   + 
Sbjct: 180 FLLAEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTR-VSELASAT 238

Query: 261 MKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLA 320
           +KRV LE GGKSA I+  D  D   A        + N GQ C A TR+L+  +   E   
Sbjct: 239 VKRVALELGGKSAAIILDDA-DFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEAAK 297

Query: 321 LLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAAIG 380
           L  + AQ ++ G P+    T+G L      D V  +I +G ++G  LL G  A L   + 
Sbjct: 298 LAVEAAQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTG-GADLPEGVN 356

Query: 381 -------PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRD 433
                  PTIF  V P++S+++EEIFGPVL +  +  EE A+ +AN + YGL   VW+  
Sbjct: 357 PDGYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWSAT 416

Query: 434 LSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489
              A +++RR++ G V +N     +M  PFGGYKQSGNGR+   + LE F E K +
Sbjct: 417 DEHAEQVARRMRTGQVEING-GTFNMYAPFGGYKQSGNGRELGKYGLEDFLEFKAM 471


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: 515
Number of extensions: 22
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: 479
Length adjustment: 34
Effective length of query: 461
Effective length of database: 445
Effective search space:   205145
Effective search space used:   205145
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 Apr 09 2024. 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