GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Sinorhizobium fredii NGR234

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_015886765.1 NGR_RS03130 aldehyde dehydrogenase family protein

Query= curated2:Q2SXN9
         (487 letters)



>NCBI__GCF_000018545.1:WP_015886765.1
          Length = 475

 Score =  211 bits (537), Expect = 4e-59
 Identities = 161/466 (34%), Positives = 233/466 (50%), Gaps = 33/466 (7%)

Query: 3   ELFIDGAWVD-GAGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDA 61
           + +IDG WV+          +P T + +   A  SA D E+AVA+ARRAFA++S      
Sbjct: 6   KFYIDGEWVEPSVSKTLEVIDPSTEQPMGTIALGSAADAEKAVAAARRAFASYSQTSKQE 65

Query: 62  RCTIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASM-AAKVDISITAYHERTGEK 120
           R  +++R   +L  R + L  +I RE G PL  AR E A + AA  + +I ++     + 
Sbjct: 66  RVELLRRILTILKRRNDELGDIISREMGAPLAMARAEQAGIGAAHFEQAIKSFETFAFD- 124

Query: 121 RAPMADGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARA 180
                 G   + H P GVVA+  P+N+P +     +  AL  G T+V KPSE+AP  A  
Sbjct: 125 ---YMQGTTRIVHEPVGVVAMITPWNWPINQIACKVAAALATGCTMVLKPSEIAPFNAVL 181

Query: 181 TVEIWRDAGLPAGVLNLVQGEKDT-GVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEI 239
             EI  +AG+P GV NLVQG+  T G ALA+H  +D + FTGS+  G  + +     P +
Sbjct: 182 FAEIMDEAGVPKGVFNLVQGDGPTVGAALASHPDVDMVSFTGSTRAGIAVAQ--AAAPTV 239

Query: 240 V-LALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVAR 298
             +  E+GG +P ++    D  AAV   ++  F ++GQ CT   R+LVP         A 
Sbjct: 240 KRVHQELGGKSPNIILRSADFPAAVAAGVRRCFGNSGQTCTAPTRMLVP---------AE 290

Query: 299 LADVASKITASVFDA-------DPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQ 351
             D A  I A   DA       D +  +G V SA    ++ A   R +  GA  +     
Sbjct: 291 RMDEAGAIAARQADALVVGPPSDSRTDLGPVASAAQFDKIQALIERGIAEGAELVAGGLG 350

Query: 352 RDPALG---FVNAAIL-DVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAG 407
           R   L    +V   +   VTN   +  EE FGP+  I+ Y   D+AIA ANDT +GL+A 
Sbjct: 351 RPSHLNAGYYVRPTVFARVTNQMSIAREEIFGPVLSIIGYDSEDEAIAVANDTPYGLAAY 410

Query: 408 LLADDEQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHR 453
           +  D ++        +R+G V  N  ++G  SAAPFGG  +SGN R
Sbjct: 411 IQGDPKET-RALAGKLRSGTVRLN--SSGWDSAAPFGGYKQSGNGR 453


Lambda     K      H
   0.320    0.134    0.402 

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: 491
Number of extensions: 27
Number of successful extensions: 4
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: 487
Length of database: 475
Length adjustment: 34
Effective length of query: 453
Effective length of database: 441
Effective search space:   199773
Effective search space used:   199773
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: 51 (24.3 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