GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Sinorhizobium meliloti 1021

Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate SMa0260 SMa0260 GabD3 succinate-semialdehyde dehdyrogenase

Query= curated2:Q9AAL5
         (472 letters)



>FitnessBrowser__Smeli:SMa0260
          Length = 487

 Score =  190 bits (483), Expect = 8e-53
 Identities = 158/477 (33%), Positives = 219/477 (45%), Gaps = 46/477 (9%)

Query: 2   SASRLISRDPYTGEAIADFAVNDARSIDAACHSARAAFAEWAMTPLAERRAIALRFAETV 61
           S S +   DP TG  +A+ A         A  +A AA A W  TP  +R  I  R+ + +
Sbjct: 28  SGSGITVLDPSTGNLLAEVADASIEDAQRAVDAADAAAAGWRATPARQRSEILRRWYQLM 87

Query: 62  RARREEIATLIARETGKPMWEALTEADSVAAKVAISIRAQDERA----GE-RSEPMADAT 116
               EE+ATLIA E GK    AL +A    A  A   R   E A    GE R  P     
Sbjct: 88  TQHAEELATLIALENGK----ALADARGEVAYAAEFFRWYAEEATRIPGEFRHTPSGSHN 143

Query: 117 ARLAHRPHGVLAVIGPFNFPMHLANGHIVPALLAGNAVVFKPSEKTPACGQLMGELWRAA 176
             + H P G+  +I P+NFP  +A   I PAL AG  V+ KP+ +TP     M  L   A
Sbjct: 144 ILVDHEPIGIAVLITPWNFPAAMATRKIGPALAAGCTVILKPASETPLTAYAMARLGEEA 203

Query: 177 GLPDHVLTIVIGGGEAG--EALVRHEALDGVLFTGGVQAGRAIHRALADAPHKIL--ALE 232
           G+P  V+ ++      G   A++    +  + FTG    GR +   LA+A   ++  ++E
Sbjct: 204 GVPPGVVNVLTTSNPGGITNAMLADPRVRKLSFTGSTGVGRVL---LAEAAKSVVSCSME 260

Query: 233 LGGNAPLVVWDVADIEAAAHLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMD 292
           LGGNAP +V+D AD+E A    + +    AG+ CT A R  +  G   DA +  LT  M 
Sbjct: 261 LGGNAPFIVFDDADLEVALDGAMIAKMRNAGEACTAANRFYVQAGIH-DAFVAGLTARMK 319

Query: 293 RLVIGGPFQSPAPFMGPVIDAHA-------AAQVLAAQDRMTADGGRPLRLAAVREARSA 345
            L + GP   P    GP+I  +A        ++ LAA  R T  GG+PL           
Sbjct: 320 SLKL-GPGYDPETQCGPMITQNAVRKIDRLVSEALAAGARATT-GGKPL------TENGY 371

Query: 346 LLSPGLIE--LTDAPLRDEEIFGPLLQVRRAADFDAALALANATRFGLAAGLISDDEALY 403
              P ++E    +A +  EEIFGP+  V +    D A+ LAN T +GLAA + S D    
Sbjct: 372 FYPPTVLENVPVNASIAREEIFGPVAPVYKFESDDEAIRLANNTEYGLAAYIYSRDLKRA 431

Query: 404 RRFWTSVRAGIVNWNRPTTGASSAAPFGGVGGSGNHRPSA-----------YYAADY 449
            +    +  G++  NR    +  AAPFGGV  SG  R              Y+A DY
Sbjct: 432 MKVGKRIETGMLGINRGLM-SDPAAPFGGVKQSGLGREGGVTGILEFMEPKYFAVDY 487


Lambda     K      H
   0.320    0.135    0.400 

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: 603
Number of extensions: 27
Number of successful extensions: 5
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: 472
Length of database: 487
Length adjustment: 34
Effective length of query: 438
Effective length of database: 453
Effective search space:   198414
Effective search space used:   198414
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 Sep 17 2021. 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