GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Methylocystis bryophila S285

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein

Query= BRENDA::C6KEM4
         (506 letters)



>NCBI__GCF_002117405.1:WP_085772038.1
          Length = 506

 Score =  342 bits (878), Expect = 1e-98
 Identities = 200/498 (40%), Positives = 287/498 (57%), Gaps = 23/498 (4%)

Query: 13  FIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQWSRAP 72
           FIGG W  P  G     ++P T   I  +  G A DVE+A+ AA  A  +D    W + P
Sbjct: 22  FIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHKA--KDA---WGKTP 76

Query: 73  GAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEASG-DMDDVAACFEYYADLAEALD 131
            A RAN L  IA ++ D  S LAL+ET+D+GKP+ E +  D+      F Y+A    A +
Sbjct: 77  AAERANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQE 136

Query: 132 GKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKPSEL 191
           G     +S    +  +Y   EP+GVVG I PWN+P+LMA WK++PALAAG   +LKP+E 
Sbjct: 137 GS----LSEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQ 192

Query: 192 ASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGKRIMTS 251
             +S L +  +  ++ LPPGVLNI+ G G EAG PL+S+  + K+AFTG T TG+ IM  
Sbjct: 193 TPMSILAVAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQY 251

Query: 252 AAQMVKPVSLELGGKSPLIVFDDI-----GDIDKAVEWTMFGIFA-NAGQVCSATSRLLL 305
           AA+ + PV+LELGGKSP I F D+       +DKA+E   F  FA N G+VC+  SR L+
Sbjct: 252 AAENLIPVTLELGGKSPNIFFADVMAEDDAFLDKALEG--FASFALNQGEVCTCPSRALV 309

Query: 306 HEKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATILYG 365
              I  KF+++ +A    I+   PL+    +G+  S  Q EKI  ++   R EGA +L G
Sbjct: 310 QRSIYDKFMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIG 369

Query: 366 GGRPQ---HLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHY 422
           G R      L+ G++++PT + +    M+++QEE+FGPV+ V  F T+ EA+++ANDT Y
Sbjct: 370 GERSVLEGELKEGYYMQPTAL-EGHNRMRVFQEEIFGPVVSVTTFETEEEALQIANDTLY 428

Query: 423 GLAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNY 482
           GL   + + D  R  R  +A+ +G +W NC       A +GG K+SG GRE  +  LD+Y
Sbjct: 429 GLGAGLWTRDGSRAYRCGRAIRAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHY 488

Query: 483 LTVKQVTKYCSDEPWGWY 500
              K +    S +  G +
Sbjct: 489 QQTKNLLVSYSPKALGLF 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: 655
Number of extensions: 30
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.

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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