GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Lutibaculum baratangense AMV1

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_023432018.1 N177_RS09120 aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_000496075.1:WP_023432018.1
          Length = 492

 Score =  347 bits (889), Expect = e-100
 Identities = 200/485 (41%), Positives = 292/485 (60%), Gaps = 12/485 (2%)

Query: 16  LAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDW 75
           +A E ++ I GE+T  + +E  ++V+P TQ   A + +    D+ RA+  A   +    W
Sbjct: 1   MAAEYQMLIGGEWTGGSGSERLDSVNPYTQEVWATLPQAGDADVARAIEIAHDTYV-SVW 59

Query: 76  SLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAI 135
              +   R  +LN+LADL+E +  +LA ++T D GK IR +    +  AAR  R++A   
Sbjct: 60  RGVNGRDRALMLNRLADLVEQNGPDLARIDTTDNGKVIRET-GSQMKFAARNYRYFAGLA 118

Query: 136 DKVYGEVATTSSHE-LAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSE 194
           DK+ G      + E L   + EP+GV   I  WN PL L   KL PALAAGN+V++KPSE
Sbjct: 119 DKLQGNTIPLDNGEMLDYTIVEPLGVAVLITAWNSPLPLLANKLAPALAAGNTVVIKPSE 178

Query: 195 KSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLK 254
            + +S +    L  EAG PDGV+N+VTG G   G AL+ H  +  I+FTG   T +++L 
Sbjct: 179 HASISTLAFGRLIAEAGFPDGVVNIVTGDGR-IGPALTTHKRVKKISFTGGLPTARRIL- 236

Query: 255 DAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESI 314
           +A    +  V  E GGKS NI+F D  DL+ A +   AGIF   GQ CIAG+RLL++ SI
Sbjct: 237 EAAARRLVPVTTELGGKSPNIIFEDA-DLKAAVNGAVAGIFGASGQTCIAGSRLLVQSSI 295

Query: 315 ADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG-QLLLDGRNA 373
            DE    + ++ +  + G+PLDPAT MG + + A  D + S I + E++G +L L GR A
Sbjct: 296 YDEVCDRVLEKVRGIRLGNPLDPATEMGPVANRAQFDRILSLIAQAENEGAKLALGGRQA 355

Query: 374 ---GLAAA--IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAA 428
              GL     I PT+  DV+P+ +++R+E+FGPVL + RF  E  A+++ANDS YGL A 
Sbjct: 356 TGPGLERGFFIEPTVLKDVEPSLTIARDEVFGPVLCILRFEDEADAVRIANDSDYGLAAG 415

Query: 429 VWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKT 488
           VWT D+ RAHRM+R ++AG V+VN Y    +  PFGG K SG+GR++S H L ++T++K 
Sbjct: 416 VWTNDVRRAHRMAREIEAGLVWVNTYRASYVGAPFGGTKLSGHGRERSWHTLMEYTQVKN 475

Query: 489 IWISL 493
           + + L
Sbjct: 476 VMLDL 480


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: 631
Number of extensions: 27
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: 492
Length adjustment: 34
Effective length of query: 461
Effective length of database: 458
Effective search space:   211138
Effective search space used:   211138
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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