GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Methylocystis bryophila S285

Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein

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



>NCBI__GCF_002117405.1:WP_085772038.1
          Length = 506

 Score =  334 bits (856), Expect = 5e-96
 Identities = 191/496 (38%), Positives = 279/496 (56%), Gaps = 17/496 (3%)

Query: 2   KQYRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRT 59
           K+Y N+I G+WV       FD+++P+ G  + QV       V+ A+ A H A + AWG+T
Sbjct: 17  KRYDNFIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHKA-KDAWGKT 75

Query: 60  TVAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTA 119
             AERA +L +IA  +D         E  D GKP+   +  DIP    +FR FA  L+  
Sbjct: 76  PAAERANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQ 135

Query: 120 PLDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSE 179
                + D    A    Y   +PLGVVG I PWN P+L+  WK++PALA GN VV KP+E
Sbjct: 136 EGSLSEIDHDTVA----YHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAE 191

Query: 180 ETPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIM 239
           +TP +   +AE++  + +PPGV N+V+GFG + AG+ + +N  I  I FTGE+ TG  IM
Sbjct: 192 QTPMSILAVAELIADL-LPPGVLNIVNGFGVE-AGKPLASNKRIAKIAFTGETTTGRLIM 249

Query: 240 RAAATHVKPVSFELGGKNAAIIFADCDFE------KMIDGMMRAVFLHSGQVCLCAERVY 293
           + AA ++ PV+ ELGGK+  I FAD   E      K ++G   +  L+ G+VC C  R  
Sbjct: 250 QYAAENLIPVTLELGGKSPNIFFADVMAEDDAFLDKALEGFA-SFALNQGEVCTCPSRAL 308

Query: 294 VERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLV 353
           V+R IY++F++  + RV  ++ G P D  T +G   S +  +K+LSY  + R+EGA+VL+
Sbjct: 309 VQRSIYDKFMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLI 368

Query: 354 GGGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTK 413
           GG           G++++PT + G     R  +EE+FGP+  V+ F+TE EA+ +ANDT 
Sbjct: 369 GGERSVLEGELKEGYYMQPTALEG-HNRMRVFQEEIFGPVVSVTTFETEEEALQIANDTL 427

Query: 414 YGLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNF 473
           YGL A  WT + +R +R   A+R G  W N +        FGG   SGIGRE     L+ 
Sbjct: 428 YGLGAGLWTRDGSRAYRCGRAIRAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDH 487

Query: 474 YSELTNVCVRIDQEAV 489
           Y +  N+ V    +A+
Sbjct: 488 YQQTKNLLVSYSPKAL 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: 584
Number of extensions: 30
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