GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Methylocapsa aurea KYG

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_000746085.1:WP_036262823.1
          Length = 506

 Score =  332 bits (851), Expect = 2e-95
 Identities = 189/483 (39%), Positives = 281/483 (58%), Gaps = 20/483 (4%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           FI G++  A + +TFE + P+    +  +AR  + D++ A+ AA     RG W  +SPA+
Sbjct: 22  FIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAA--RGAWGRTSPAE 79

Query: 83  RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142
           R   L ++AD +E   + LA++ET+D GKPIR +   D+P A    R++A  +    G +
Sbjct: 80  RSLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEGGI 139

Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202
           +      +A    EP+GV+A I+PWNFPLL+  WKL PALAAGN VILKP+E++P+S + 
Sbjct: 140 SEIDHDTVAYHFHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQTPMSVMV 199

Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262
           L  +  +  LP GVLNV+ GFG EAG+ L+++  I  +AFTG T TG+ +++ A + N+ 
Sbjct: 200 LVDMIGDL-LPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTGETTTGRLIMQYASE-NII 257

Query: 263 RVWLEAGGKSANIVFADCPDLQQAASATAAGIF----YNQGQVCIAGTRLLLEESIADEF 318
            V LE GGKS NI FAD  D        A   F     NQG+VC   +R L++E I D F
Sbjct: 258 PVTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFALNQGEVCTCPSRALVQEKIYDRF 317

Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAA 378
           +     + +  + G+PLDPAT +G        + + S++  G  +G  +L G   G  A 
Sbjct: 318 MERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAG---GGRAD 374

Query: 379 IGPTI---------FVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAV 429
           +GP +          ++      + +EEIFGPVL VT F  +E+AL++AND+ YGLGA V
Sbjct: 375 VGPELAGGFYVQPTILEGHNKMRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYGLGAGV 434

Query: 430 WTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489
           WTR+ +RA+R  R ++AG V+ N Y+       FGGYKQSG GR+     L+ + + K +
Sbjct: 435 WTRNGTRAYRFGRAIEAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQKTKNM 494

Query: 490 WIS 492
            +S
Sbjct: 495 LVS 497


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: 554
Number of extensions: 18
Number of successful extensions: 6
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: 506
Length adjustment: 34
Effective length of query: 461
Effective length of database: 472
Effective search space:   217592
Effective search space used:   217592
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