GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Methylocapsa aurea KYG

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein

Query= BRENDA::C6KEM4
         (506 letters)



>NCBI__GCF_000746085.1:WP_036262823.1
          Length = 506

 Score =  342 bits (878), Expect = 1e-98
 Identities = 207/503 (41%), Positives = 289/503 (57%), Gaps = 23/503 (4%)

Query: 8   PRRGLFIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQ 67
           P    FIGG W     G+    ++P     I  +   +AEDVE+A+ AA  A        
Sbjct: 17  PHYDNFIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAARGA----- 71

Query: 68  WSRAPGAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEA-SGDMDDVAACFEYYADL 126
           W R   A R+  L  IA +I+ +   LA++ET+D+GKP+ E  + D+      F Y+A  
Sbjct: 72  WGRTSPAERSLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGC 131

Query: 127 AEALDGKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTIL 186
             A +G     IS    +  +Y   EP+GVV  I PWN+PLLMA WK+APALAAG   IL
Sbjct: 132 LRAQEGG----ISEIDHDTVAYHFHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVIL 187

Query: 187 KPSELASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGK 246
           KP+E   +S + L  +  ++ LPPGVLN+I G G EAG PL+ +  + KVAFTG T TG+
Sbjct: 188 KPAEQTPMSVMVLVDMIGDL-LPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTGETTTGR 246

Query: 247 RIMTSAAQMVKPVSLELGGKSPLIVFDDIGD-----IDKAVEWTMFGIFA-NAGQVCSAT 300
            IM  A++ + PV+LELGGKSP I F D+ D      DKA+E   F +FA N G+VC+  
Sbjct: 247 LIMQYASENIIPVTLELGGKSPNIFFADVADEDDDFFDKALEG--FSMFALNQGEVCTCP 304

Query: 301 SRLLLHEKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGA 360
           SR L+ EKI  +F++R VA  K IK  +PL+    +G+  S  Q EKI  ++   R EGA
Sbjct: 305 SRALVQEKIYDRFMERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGA 364

Query: 361 TILYGGGRPQ---HLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELA 417
            +L GGGR      L  GF+++PTI+ +    M+I+QEE+FGPV+ V  F+ D EA+E+A
Sbjct: 365 KVLAGGGRADVGPELAGGFYVQPTIL-EGHNKMRIFQEEIFGPVLSVTSFKDDEEALEIA 423

Query: 418 NDTHYGLAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEW 477
           NDT YGL   V + +  R  R  +A+ +G +W NC       A +GG K+SG GRE  + 
Sbjct: 424 NDTLYGLGAGVWTRNGTRAYRFGRAIEAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKM 483

Query: 478 GLDNYLTVKQVTKYCSDEPWGWY 500
            LD+Y   K +    S +  G++
Sbjct: 484 MLDHYQKTKNMLVSYSPKALGFF 506


Lambda     K      H
   0.318    0.136    0.418 

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: 671
Number of extensions: 31
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: 506
Length of database: 506
Length adjustment: 34
Effective length of query: 472
Effective length of database: 472
Effective search space:   222784
Effective search space used:   222784
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.

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