GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Lentibacillus jeotgali Grbi

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_010531933.1 ON01_RS15200 aldehyde dehydrogenase family protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_4383
         (497 letters)



>NCBI__GCF_000224785.1:WP_010531933.1
          Length = 480

 Score =  333 bits (855), Expect = 6e-96
 Identities = 187/477 (39%), Positives = 276/477 (57%), Gaps = 8/477 (1%)

Query: 23  FINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSK 82
           +ING++ D+   ET +  +P  G ++  I      D  +AV  A+ +F S  W R+ P +
Sbjct: 7   YINGKWEDSHDKETINVNNPSTGEVMTTIPRGKNDDVDKAVRAAKDSFVSEEWRRVKPFE 66

Query: 83  RKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEV 142
           R   +      LK++ +ELA LET+D+GKP++     D+  A +   + G A DK+  + 
Sbjct: 67  RGRILCEVVAQLKENRDELARLETMDVGKPLTQGY-ADIDAAIRYFEFYGGAADKVMGDT 125

Query: 143 AATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALR 202
                  +  V REP+GV   IVPWN+P+ +    +  A++ GN+VV+K +E +PLTA +
Sbjct: 126 IPIEDGLIDYVIREPIGVTAHIVPWNYPIQILSRSVAAAIAMGNTVVVKSAEDTPLTAAK 185

Query: 203 IAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMK 262
           IA    +  +P+GV N + GYG+  G AL+ H  ++ L FTGS       +  +  SN+ 
Sbjct: 186 IAEYFDQTDLPEGVFNHVTGYGYEAGAALSSHPLINHLTFTGSVGTG-TAVANAATSNVV 244

Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTFLPLV 322
            + LE GGKSPNIVF+D  D+  A E    AI  N G+ C+AGSRLL+E S K TFL  +
Sbjct: 245 PVTLELGGKSPNIVFSDC-DVDKAVEGVVKAIIQNAGQTCSAGSRLLIEESFKQTFLDKL 303

Query: 323 IEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRILEE--TGG 380
           +   K    G  +D   N+G +++ +Q + +L +I     +G  ++ GGKR+  E     
Sbjct: 304 VNKFKTLSVGPAIDD-HNLGPILNQKQFDRILEFISLAEQEGT-VLTGGKRVKYEQYENA 361

Query: 381 TYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTKDISK 440
            Y+EPTI D +S   K AQEEIFGPVLSV  F   ++AI+IAN T YGL   +WTKDI+K
Sbjct: 362 CYLEPTIIDNLSLNSKAAQEEIFGPVLSVFTFKNEQEAIDIANSTDYGLVTGIWTKDINK 421

Query: 441 AHLTAKALRAGSVWVNQYD-GGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKSTWIK 496
           AHL    + +G V++N Y  GG +  PFGG+K+SG GR+K   A   YT++K+  IK
Sbjct: 422 AHLLMSRIDSGQVFINNYGAGGGIQMPFGGYKKSGFGREKGWIALYNYTQVKNVAIK 478


Lambda     K      H
   0.316    0.132    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: 582
Number of extensions: 26
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: 497
Length of database: 480
Length adjustment: 34
Effective length of query: 463
Effective length of database: 446
Effective search space:   206498
Effective search space used:   206498
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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