GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Methylocystis bryophila S285

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_002117405.1:WP_085772038.1
          Length = 506

 Score =  337 bits (864), Expect = 6e-97
 Identities = 194/492 (39%), Positives = 289/492 (58%), Gaps = 20/492 (4%)

Query: 15  SLAIENRL--FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFER 72
           S+AI+ R   FI G++ A    E F+ + P+T  P+ ++ARG++ D++ A+ AA     +
Sbjct: 12  SVAIKKRYDNFIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHKA--K 69

Query: 73  GDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYA 132
             W  +  A+R  +LNK+A  ++ +   LAL+ET+D GKPIR +   DIP A    R++A
Sbjct: 70  DAWGKTPAAERANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFA 129

Query: 133 EAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKP 192
             +    G ++      +A    EP+GV+  I+PWNFP+L+  WKL PALAAGN V+LKP
Sbjct: 130 GCLRAQEGSLSEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKP 189

Query: 193 SEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQL 252
           +E++P+S + +A L  +  LP GVLN+V GFG EAG+ L+ +  I  IAFTG T TG+ +
Sbjct: 190 AEQTPMSILAVAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLI 248

Query: 253 LKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQA----ASATAAGIFYNQGQVCIAGTRL 308
           ++ A + N+  V LE GGKS NI FAD      A    A    A    NQG+VC   +R 
Sbjct: 249 MQYAAE-NLIPVTLELGGKSPNIFFADVMAEDDAFLDKALEGFASFALNQGEVCTCPSRA 307

Query: 309 LLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG-QLL 367
           L++ SI D+F+     +    + GHPLDPAT +G        + + S++  G  +G ++L
Sbjct: 308 LVQRSIYDKFMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVL 367

Query: 368 LDGRNAGLAAAIGPTIFVDVDPNA-------SLSREEIFGPVLVVTRFTSEEQALQLAND 420
           + G  + L   +    +  + P A        + +EEIFGPV+ VT F +EE+ALQ+AND
Sbjct: 368 IGGERSVLEGELKEGYY--MQPTALEGHNRMRVFQEEIFGPVVSVTTFETEEEALQIAND 425

Query: 421 SQYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHAL 480
           + YGLGA +WTRD SRA+R  R ++AG V+ N Y+       FGGYKQSG GR+     L
Sbjct: 426 TLYGLGAGLWTRDGSRAYRCGRAIRAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMML 485

Query: 481 EKFTELKTIWIS 492
           + + + K + +S
Sbjct: 486 DHYQQTKNLLVS 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: 532
Number of extensions: 20
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