GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Novosphingobium fuchskuhlense FNE08-7

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_067911749.1 AQZ52_RS13615 aldehyde dehydrogenase family protein

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_001519075.1:WP_067911749.1
          Length = 486

 Score =  285 bits (730), Expect = 2e-81
 Identities = 188/460 (40%), Positives = 257/460 (55%), Gaps = 11/460 (2%)

Query: 36  TFETVDPVT-QAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLM 94
           TFET  P      LA IARG +     A  AA   F    W+  + A+R   L++LADL+
Sbjct: 28  TFETRCPFEWDRKLADIARGDAQTAALAAEAASAAFPA--WAALTAAERGVYLHRLADLI 85

Query: 95  EAHAEELALLETLDTGKPIRH-SLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMI 153
           EA+ E+LA++E LD G  +    LR  + GAA   R YA+ +   + E   +S   L  +
Sbjct: 86  EANVEKLAVVECLDMGMLLESLRLRVILRGAAN-FRTYAD-LAAHHEERVWSSRGTLNRV 143

Query: 154 VREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLP 213
           +R P G    I PWN P +L+ WK  PALAAGN+VILKP++ SPLSA  LA L  EAG+P
Sbjct: 144 IRMPAGPALIITPWNAPFMLSTWKCAPALAAGNTVILKPADWSPLSASVLADLIHEAGIP 203

Query: 214 DGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSA 273
            GV N+V G G E G AL+    I  I+FTGS  T + + + A + N+     E GGKS 
Sbjct: 204 AGVFNIVQGLGAELGNALTSDPRIKRISFTGSVPTARVIGRAAAE-NIVPFTAELGGKSP 262

Query: 274 NIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGH 333
            +VFAD  D+  AA+  AAG F + GQVC+AGTR+++EES+ + FL            G 
Sbjct: 263 LLVFADA-DI-DAAAKKAAGQFDDSGQVCMAGTRIIVEESVKEAFLEKFHGYTDAHVMGD 320

Query: 334 PLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAA--IGPTIFVDVDPNA 391
             DPATTM  LI   HA+ V  FI    + G  ++ G       A  I PT+ V  D  +
Sbjct: 321 SRDPATTMSALIHPVHAERVLGFIDRARAAGDTVVRGGKRWKEGANWIEPTLIVPKDNQS 380

Query: 392 SLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSVFV 451
            + + E+FGPVL    F  E + + LAN + YGL   V+T    RA R+ R ++ G+V+V
Sbjct: 381 EVVQNEVFGPVLTFQTFRDEAEGVALANSTAYGLSGIVYTGSEDRAQRVGRAVRGGTVWV 440

Query: 452 NNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491
           N +   D+T PFGG   SG GR+   +AL+  ++LKT+ I
Sbjct: 441 NTFLVRDLTAPFGGIGISGIGREGGDYALDFHSDLKTLQI 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: 597
Number of extensions: 27
Number of successful extensions: 5
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: 486
Length adjustment: 34
Effective length of query: 461
Effective length of database: 452
Effective search space:   208372
Effective search space used:   208372
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.

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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