GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Sphingomonas koreensis DSMZ 15582

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__Korea:Ga0059261_1680
          Length = 469

 Score =  275 bits (704), Expect = 2e-78
 Identities = 178/477 (37%), Positives = 267/477 (55%), Gaps = 19/477 (3%)

Query: 21  RLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSP 80
           RL ++G+  A AE  TF  +DP T  P A      + D+D A++AAR  F    W+ +  
Sbjct: 5   RLIVDGKPLAMAE--TFPVIDPATGRPFADAPLASTADLDAAVAAARRAFP--GWAATPI 60

Query: 81  AKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGA---ARAIRWYAEAIDK 137
             R A +  +AD +EA  +ELA L + + GKP+ +++  +I GA   ARA      A+D 
Sbjct: 61  EDRAAAILAIADSIEAAKDELARLLSAEQGKPVPNAV-GEIMGALAWARATAGLRPAVD- 118

Query: 138 VYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSP 197
               V          + R+P+GV+A+I PWNFP+++  W + P L AGN+V++KPS  +P
Sbjct: 119 ----VLKDDDSVRVEVHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTP 174

Query: 198 LSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAG 257
           L+A+R+  +A  A LP GVLN VTG   E G+A++ H  ID I FTGST TG+ ++ D G
Sbjct: 175 LAALRMVEIAN-AHLPPGVLNSVTG-EVEIGRAIASHPGIDKIVFTGSTPTGRSIMAD-G 231

Query: 258 DSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADE 317
            +N+KR+ LE GG  A IV  D  D+ + A+   A  F N GQ+C A  R+ + ESI D 
Sbjct: 232 AANLKRLTLELGGNDAAIVLPDA-DVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDA 290

Query: 318 FLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA--GL 375
               L + A+    G   D A+  G + +    D V +   +  + G   L G  A  G 
Sbjct: 291 LAEKLAEMARTAVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREGD 350

Query: 376 AAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLS 435
                 ++ VDV     +  EE FGP+L V R++  E AL  AN ++ GLG +VW+ D +
Sbjct: 351 GYFFPLSVVVDVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPA 410

Query: 436 RAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWIS 492
            A   ++RL+AG+V+VN++      VPFGG KQSG G +  L+ LE++ +L+T+ ++
Sbjct: 411 AALAFAQRLEAGTVWVNDHASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTVRVA 467


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: 573
Number of extensions: 25
Number of successful extensions: 8
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: 469
Length adjustment: 34
Effective length of query: 461
Effective length of database: 435
Effective search space:   200535
Effective search space used:   200535
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