GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Lutibaculum baratangense AMV1

Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate WP_023433595.1 N177_RS16800 aldehyde dehydrogenase family protein

Query= curated2:Q9AAL5
         (472 letters)



>NCBI__GCF_000496075.1:WP_023433595.1
          Length = 499

 Score =  206 bits (525), Expect = 1e-57
 Identities = 149/449 (33%), Positives = 226/449 (50%), Gaps = 20/449 (4%)

Query: 10  DPYTGEAIADFAVNDARSIDAACHSARAAFAEWAMTPLAERRAIALRFAETVRARREEIA 69
           +P+ G+ +A+ +   A  +D AC ++  A  EWA    A R  I ++  + V AR+EEI 
Sbjct: 35  NPFNGDTLAEISTASAEDVDEACRASLEAQREWAALVPAARAEIMMKATQIVEARQEEIV 94

Query: 70  TLIARETGKPMWEALTEADSVAA--KVAISIRAQDERAGERSEPMADATARLAHRPHGVL 127
           + + RE G    +A  E   V    K A S+    E     ++ +    +R+  +P GV+
Sbjct: 95  SWLVREAGSTRLKATMEWTFVQGVFKEAASLPHMVEGRILPND-IPGKESRVYRKPVGVV 153

Query: 128 AVIGPFNFPMHLANGHIVPALLAGNAVVFKPSEKTPACGQLM-GELWRAAGLPDHVLTIV 186
           A+I P+N+P  L    + PAL  GN VV KP+  TP  G L+  ++   AGLP+ +L+++
Sbjct: 154 ALISPWNWPFQLTARTLAPALAVGNGVVVKPASDTPITGGLLFAKILEEAGLPEGLLSVL 213

Query: 187 IG-GGEAGEALVRHEALDGVLFTGGVQAGRAIHRALADAPH-KILALELGGNAPLVVWDV 244
            G G E G  L+ HE    V FTG    GR I +A AD    K L LELGGN+P+VV D 
Sbjct: 214 PGPGSEVGNTLIMHEIPRVVSFTGSTLVGRGIAKASADGKKIKRLELELGGNSPIVVLDD 273

Query: 245 ADIEAAAHLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMDR---LVIGGPFQ 301
           AD++ A    V   ++  GQ C  + RL++ E        E ++  +DR   L +G P  
Sbjct: 274 ADLDLAVEASVFGKFLHQGQICMISNRLVVTEKIYD----EFVSRFVDRVKGLKVGDP-S 328

Query: 302 SPAPFMGPVIDAHAAAQVLAAQDRMTADGGRPLRLAAVREARSALLSPGLIE--LTDAPL 359
            P  F+GP+I+      V+   ++    G +  R+ A  E    +L P +     TD+ L
Sbjct: 329 DPDTFIGPIINRSQLDSVVEKIEK----GKKGARMLAGGEPDGQVLPPHVFADIPTDSAL 384

Query: 360 RDEEIFGPLLQVRRAADFDAALALANATRFGLAAGLISDDEALYRRFWTSVRAGIVNWNR 419
             EEIFGP+  + +A D   AL +AN T +GL++ + + D     RF  S+ AG+ + N 
Sbjct: 385 AQEEIFGPVAPILKARDEQDALKIANDTEYGLSSAVFTRDVEKGTRFARSIEAGMAHVND 444

Query: 420 PTTGASSAAPFGGVGGSGNHRPSAYYAAD 448
                    PFGG   SG  R +  +A D
Sbjct: 445 QPVNDLPFNPFGGEKNSGIGRFNGRWAID 473


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: 575
Number of extensions: 39
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: 499
Length adjustment: 34
Effective length of query: 438
Effective length of database: 465
Effective search space:   203670
Effective search space used:   203670
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 Sep 24 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