GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Sinorhizobium fredii NGR234

Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_012708832.1 NGR_RS22740 aldehyde dehydrogenase family protein

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



>NCBI__GCF_000018545.1:WP_012708832.1
          Length = 502

 Score =  341 bits (875), Expect = 3e-98
 Identities = 196/496 (39%), Positives = 285/496 (57%), Gaps = 19/496 (3%)

Query: 3   QYRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTT 60
           +Y N+I GEW E  + R FD+  PV G  + Q+  +D   ++ A+ A HAA +  WGRT+
Sbjct: 14  KYGNFIGGEWREPVAGRYFDNTTPVTGGSLCQIARSDAADIELALDAAHAA-KEKWGRTS 72

Query: 61  VAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAP 120
             ER+ IL +IA  ++   +    AE  D GKP+      DIP    +FR FA  ++   
Sbjct: 73  TTERSNILMKIAARMEDNLELLARAETWDNGKPIRETMAADIPLAIDHFRYFAACIRAQE 132

Query: 121 LDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEE 180
               + D    A    Y   +PLGVVG I PWN P+L+  WK+APALA GN VV KP+E+
Sbjct: 133 GSIGEIDHDTVA----YHFHEPLGVVGQIIPWNFPILMAAWKVAPALAAGNCVVLKPAEQ 188

Query: 181 TPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMR 240
           TP +  +LAE++  + +PPGV N+V+GFG + AG+ + T+  I  I FTGE+ TG  IM+
Sbjct: 189 TPASILILAELIADL-LPPGVLNIVNGFGLE-AGKPLATSPRIAKIAFTGETTTGRLIMQ 246

Query: 241 AAATHVKPVSFELGGKNAAIIFADC------DFEKMIDGMMRAVF-LHSGQVCLCAERVY 293
            A+ ++ PV+ ELGGK+  I FAD        F+K ++G   A+F L+ G+VC C  R  
Sbjct: 247 YASQNLIPVTLELGGKSPNIFFADVLNEDDDYFDKALEGF--AMFALNQGEVCTCPSRAL 304

Query: 294 VERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLV 353
           V+  IY+RF++  V+RV+A++ G P D  T +G   S E  +K+LSY  + ++EGA+VL 
Sbjct: 305 VQESIYDRFMERAVKRVEAIRQGNPLDSATMIGAQASGEQLEKILSYIDIGKQEGAEVLA 364

Query: 354 GGGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTK 413
           GGG          G++V+PT+  G     R  +EE+FGP+  V+ F TE EA+ +ANDT 
Sbjct: 365 GGGRNVLEGDLAGGYYVKPTVFRG-HNKMRIFQEEIFGPVVSVTTFKTEDEALEIANDTL 423

Query: 414 YGLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNF 473
           YGL A  W+ + NR +R    ++ G  W N +        FGG   SGIGRE     L+ 
Sbjct: 424 YGLGAGVWSRDANRCYRFGREIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDH 483

Query: 474 YSELTNVCVRIDQEAV 489
           Y +  N+ V    +A+
Sbjct: 484 YQQTKNMLVSYSPKAL 499


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: 580
Number of extensions: 32
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: 502
Length adjustment: 34
Effective length of query: 456
Effective length of database: 468
Effective search space:   213408
Effective search space used:   213408
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