GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Methylocapsa aurea KYG

Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-13349
         (490 letters)



>NCBI__GCF_000746085.1:WP_036262823.1
          Length = 506

 Score =  358 bits (918), Expect = e-103
 Identities = 199/494 (40%), Positives = 284/494 (57%), Gaps = 17/494 (3%)

Query: 4   YRNYINGEWVESAR--RFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTTV 61
           Y N+I G+WV + +   F++++P+DG V+  V  +  E V+ A+ A HAA RGAWGRT+ 
Sbjct: 19  YDNFIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAA-RGAWGRTSP 77

Query: 62  AERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAPL 121
           AER+  L RIAD I+++ D     E  D GKP+      D+P    +FR FA  L+    
Sbjct: 78  AERSLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEG 137

Query: 122 DTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEET 181
              + D    A    Y   +PLGVV  I PWN PLL+  WK+APALA GN V+ KP+E+T
Sbjct: 138 GISEIDHDTVA----YHFHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQT 193

Query: 182 PGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRA 241
           P +  +L +++  + +PPGV N+++GFG + AG+ +  N  I  + FTGE+ TG  IM+ 
Sbjct: 194 PMSVMVLVDMIGDL-LPPGVLNVINGFGVE-AGKPLAQNKRIAKVAFTGETTTGRLIMQY 251

Query: 242 AATHVKPVSFELGGKNAAIIFADCD------FEKMIDGMMRAVFLHSGQVCLCAERVYVE 295
           A+ ++ PV+ ELGGK+  I FAD        F+K ++G      L+ G+VC C  R  V+
Sbjct: 252 ASENIIPVTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFA-LNQGEVCTCPSRALVQ 310

Query: 296 RPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVGG 355
             IY+RF++  V RVK +K G P D  T +G   S +  +K+LSY  + R+EGA+VL GG
Sbjct: 311 EKIYDRFMERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAGG 370

Query: 356 GVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKYG 415
           G    G     GF+V+PTI+ G     R  +EE+FGP+  V+ F  + EA+ +ANDT YG
Sbjct: 371 GRADVGPELAGGFYVQPTILEG-HNKMRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYG 429

Query: 416 LSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFYS 475
           L A  WT N  R +R   A+  G  W N + L      FGG   SGIGRE     L+ Y 
Sbjct: 430 LGAGVWTRNGTRAYRFGRAIEAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQ 489

Query: 476 ELTNVCVRIDQEAV 489
           +  N+ V    +A+
Sbjct: 490 KTKNMLVSYSPKAL 503


Lambda     K      H
   0.321    0.137    0.420 

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: 592
Number of extensions: 33
Number of successful extensions: 8
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: 490
Length of database: 506
Length adjustment: 34
Effective length of query: 456
Effective length of database: 472
Effective search space:   215232
Effective search space used:   215232
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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