GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Tistlia consotensis USBA 355

Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate WP_179243903.1 B9O00_RS00790 aldehyde dehydrogenase family protein

Query= curated2:Q9AAL5
         (472 letters)



>NCBI__GCF_900177295.1:WP_179243903.1
          Length = 480

 Score =  216 bits (550), Expect = 1e-60
 Identities = 154/464 (33%), Positives = 221/464 (47%), Gaps = 23/464 (4%)

Query: 15  EAIADFAVNDARSIDAACHSARAAFAEWAMTPLAERRAIALRFAETVRARREEIATLIAR 74
           + +  +A  DA     A  +A AAF  W+ +   +R  I       + AR+EE+  L++R
Sbjct: 29  DVVGLYAQGDAAQAGQAIDAAAAAFPAWSRSTPQQRFDILDAAGTEILARKEELGRLLSR 88

Query: 75  ETGKPMWEALTEADSVAAKVAISIRAQDERAGERSEPMADAT-ARLAHRPHGVLAVIGPF 133
           E GK + E + E                  AG+R +       A     P GV+ +I P+
Sbjct: 89  EEGKTLPEGIGETVRAGQIFKFFAGEALRIAGDRIDSTRPGVIAEATREPLGVVGLITPW 148

Query: 134 NFPMHLANGHIVPALLAGNAVVFKPSEKTPACGQLMGELWRAAGLPDHVLTIVIGGGEA- 192
           NFP+ +    + PAL  GN VV KP++  P C   + ++ + AGLP  V  +V+G G   
Sbjct: 149 NFPIAIPAWKLAPALAFGNCVVMKPADLVPGCAWALADILQRAGLPKGVFNLVMGRGSVV 208

Query: 193 GEALVRHEALDGVLFTGGVQAGRAI-HRALADAPHKILALELGGNAPLVVWDVADIEAAA 251
           GEA++    +  + FTG V  GR +  R +     K   LE+GG  P VV D AD+E AA
Sbjct: 209 GEAILASPKVAAISFTGSVATGRHVARRCIEGEAMKKFQLEMGGKNPFVVLDDADLEVAA 268

Query: 252 HLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMDRLVIGGPFQSPAPFMGPVI 311
           +  +  A+ + GQRCT + RLI+ EG   D  +EALT  +  L +    +     +GPV+
Sbjct: 269 NSALNGAFFSTGQRCTASSRLIVTEGIH-DRFVEALTSKLKALKVDNALKEGTQ-IGPVV 326

Query: 312 DAHAAAQVL----AAQDR--MTADGGRPLRLAAVREARSALLSPGLIELTDAPLR--DEE 363
           D     Q L      QD     A GG  L     RE     L P L   TD  +R   EE
Sbjct: 327 DQRQLDQDLDYIKVGQDEGAKLAWGGERLN----RETEGFYLQPALFTETDNAMRINREE 382

Query: 364 IFGPLLQVRRAADFDAALALANATRFGLAAGLISDDEALYRRFWTSVRAGIVNWNRPTTG 423
           IFGP+  V R  D+D+ALA+AN T+FGL+AG+ +        F  + +AG+V  N PT G
Sbjct: 383 IFGPVASVIRVKDYDSALAVANDTQFGLSAGIATSSLKHAEHFKRNSQAGMVMVNLPTAG 442

Query: 424 ASSAAPFGGVGGSGNHRPSAYYAADYSAYPVAGLESPSPVYRLP 467
                PFGG       + S+Y A +   Y V    +    Y +P
Sbjct: 443 VDYHVPFGG------RKNSSYGAREQGRYAVEFYTTVKTAYAMP 480


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: 560
Number of extensions: 35
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: 480
Length adjustment: 33
Effective length of query: 439
Effective length of database: 447
Effective search space:   196233
Effective search space used:   196233
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