GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Pseudarthrobacter sulfonivorans Ar51

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_058929155.1 AU252_RS01160 aldehyde dehydrogenase family protein

Query= BRENDA::Q5P171
         (474 letters)



>NCBI__GCF_001484605.1:WP_058929155.1
          Length = 486

 Score =  423 bits (1087), Expect = e-123
 Identities = 210/469 (44%), Positives = 290/469 (61%), Gaps = 6/469 (1%)

Query: 6   MIINGKPVRAGSTFDVVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTPDAERKR 65
           ++I+G+ V A STFDV NPATG+V A+        +D+AVAAA  AFP W+ TP  ER  
Sbjct: 19  LVIDGQAVSAMSTFDVFNPATGQVIAKAPDASVEQLDEAVAAAARAFPAWAATPIEERAA 78

Query: 66  LMHALGAALEAHMPELMELVTKEAGKPLGGLNGVGSGMEVGGAIAWTHVTADLELPVEVI 125
           ++ A+G  +E H  + M L+T+E GKP  G        E+ G+  W    A   L  EV+
Sbjct: 79  VLAAIGDRIEEHSEQFMALLTREQGKPRAGAE-----WEIMGSAIWCREIAKQRLTPEVL 133

Query: 126 QDNDDARIEVHRKPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVVIKPSGMTPTATIRF 185
            D+D+ R+     PLGV+G+I PWN+P+++AIW + PA+ AGNT+V+KPS  TP  T++ 
Sbjct: 134 VDDDNRRVTTRYTPLGVIGAIAPWNFPILLAIWKIAPAILAGNTIVVKPSPFTPLTTLKL 193

Query: 186 VELANAILPPGVLNIVTGESGVGSAIAKHPDINKIVFTGSTPTGKNIMQNAAGNLKRLTL 245
            EL   +LP GV N+VTG   +G  +  HP I KI FTGST TG+++M +AA ++KR+TL
Sbjct: 194 AELVQDLLPAGVFNVVTGGDDLGKRMTSHPGIAKIAFTGSTETGRHVMASAAKSIKRVTL 253

Query: 246 ELGGNDAGIVLPDVDPKAIAPKLFGVGFHNNGQTCACLKRLYVHDSIYEKVCAELARIAK 305
           ELGGND  IVLPDVDP  +AP+LF   F NN Q C   KRLY+H+ +Y+ V   L   AK
Sbjct: 254 ELGGNDPAIVLPDVDPATVAPQLFWAAFQNNAQFCNATKRLYIHEDVYDVVRDALVEYAK 313

Query: 306 ETVVGDGLVEGTELGPVQNKAQLDFVQELVEDARAHGARILSGGKA-RSGGGFFFEPTVI 364
              VG+G    T+LGP+QN  Q + V+E   D    G     GG+   S  G+F   + +
Sbjct: 314 TVKVGNGAEPHTDLGPIQNAPQFEKVKEFFADCNDRGYAFALGGQIDESQPGWFIPVSFV 373

Query: 365 ADAKDGMRVVDEEQFGPVLPVIRYSDIEEVIARANNNENGLGGSIWSKDHAKAAELALRL 424
            +  +  R+V EE FGP+LP++++ D E+VI+RAN+ + GLG S+W KD      +A R+
Sbjct: 374 DNPPEDSRIVQEEPFGPILPLLKWRDEEDVISRANDTQWGLGASVWGKDEQALERIAARI 433

Query: 425 ECGTAWVNEHGAVQPDAPFGGVKQSGLGVEFGRYGLEEYTSIQTLKIMK 473
           E GT W+NE     P+  FGG KQSGLG E   +GL EYT+ QT  + K
Sbjct: 434 EAGTVWINEVHQYAPNQAFGGHKQSGLGCENSLHGLAEYTNWQTTTLNK 482


Lambda     K      H
   0.317    0.136    0.405 

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: 681
Number of extensions: 32
Number of successful extensions: 3
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: 474
Length of database: 486
Length adjustment: 34
Effective length of query: 440
Effective length of database: 452
Effective search space:   198880
Effective search space used:   198880
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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