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_015886756.1 NGR_RS03080 NAD-dependent succinate-semialdehyde dehydrogenase

Query= curated2:Q1QTQ7
         (489 letters)



>NCBI__GCF_000018545.1:WP_015886756.1
          Length = 484

 Score =  207 bits (528), Expect = 5e-58
 Identities = 162/473 (34%), Positives = 230/473 (48%), Gaps = 35/473 (7%)

Query: 4   KQQLLIDGAWVDGDAARFAKT-DPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSF 62
           +Q  +I G W+   +    +  DP S   L T       +   A+ AA  AF  W +++ 
Sbjct: 10  RQAGVIGGEWIGAASGDVVEVFDPASQAVLGTVPDMGTAETRAAIEAAETAFGPWKKKTH 69

Query: 63  AERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEV--GAMIGKVAISITAYHERT 120
           AER A++ER+   +  H E LA  +  E GKPL EAR E+  GA          A+ +  
Sbjct: 70  AERAALLERWHALMIEHLEDLALILTLEQGKPLDEARGEIRYGA----------AFVKWF 119

Query: 121 GERARDIG---------DARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVF 171
            E AR IG         D R V+     GV A+  P+NFP  +    + PAL AG  VV 
Sbjct: 120 AEEARRIGGHTIPSPTPDRRIVVLKEAVGVCAIVTPWNFPNAMITRKVAPALAAGCTVVI 179

Query: 172 KPSEQTPMTADLTLQCWLE-AGLPAGVINLVQG-AAEVGQALAGSADIDGLLFTGSAKVG 229
           KPSE TP +A L L    E AG+PAGV+N+V G    +G  +  +  +  + FTGS +VG
Sbjct: 180 KPSEFTPFSA-LALGVLAERAGIPAGVVNIVTGMPTAIGNEIMANETVRKISFTGSTRVG 238

Query: 230 GLLHRQFGGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIV 289
            LL R     V K L+LELGGN P +V D  D + AV   + S F +GGQ C CA R++V
Sbjct: 239 SLLMRGAADSV-KRLSLELGGNAPFIVFDDADLDLAVEGAIASKFRNGGQTCVCANRILV 297

Query: 290 PHGAVGDDLIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPL 349
             G V D   + L + +  ++V  P +EP      + +  A D +    +D +A+G +  
Sbjct: 298 QSG-VYDAFAEKLAARVNAMKV-GPGTEPGVAIGPMINAAAIDKIDRHVEDALAKGAKIA 355

Query: 350 SRMRRLQAGTSLLSPGLID--VTGCDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLS 407
           +R R L  G    +P ++    T   +  EE FGP+  +  +   +EAI +AN T +GL+
Sbjct: 356 ARGRSLPVGRQYTAPLVLTGATTEMLLASEETFGPVAPLFCFETEEEAITIANGTPFGLA 415

Query: 408 AGLIGGERADWDDFLLRIRAGIVNWNRQTTGASSD--APFGGIGDSGNHRPSA 458
           A                +  G+V  N   TGA S   APFGG+  SG  R  A
Sbjct: 416 AYFYTENLKRSWRVAEALEFGMVGLN---TGAISTEVAPFGGVKQSGLGREGA 465


Lambda     K      H
   0.319    0.135    0.409 

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: 639
Number of extensions: 34
Number of successful extensions: 7
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: 489
Length of database: 484
Length adjustment: 34
Effective length of query: 455
Effective length of database: 450
Effective search space:   204750
Effective search space used:   204750
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