GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Sedimenticola selenatireducens DSM 17993

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_029133105.1 A3GO_RS0108930 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>NCBI__GCF_000428045.1:WP_029133105.1
          Length = 497

 Score =  724 bits (1868), Expect = 0.0
 Identities = 346/496 (69%), Positives = 405/496 (81%)

Query: 1   MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           M  I H I GE++ D  RT  ++NP+TGE  R+V LA R T+++AI AA+AAFPAWR TP
Sbjct: 1   MNTIGHFINGEIVNDDQRTQPIYNPATGETSRQVALASRATVERAIAAAEAAFPAWRETP 60

Query: 61  PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120
           P KRAQV+FR+KQLLE + E I  LI++EHGK ++DA GEL RGIE VEYA  APE+LKG
Sbjct: 61  PLKRAQVMFRYKQLLEQHAEEICGLITDEHGKVLDDAMGELMRGIEVVEYACGAPELLKG 120

Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180
           EYS++VGP ID+WS+FQP+GVV GITPFNFP MVP+WM+P+AI CGNTFILKPSERDPS+
Sbjct: 121 EYSKSVGPAIDSWSEFQPLGVVVGITPFNFPVMVPMWMFPMAIICGNTFILKPSERDPSA 180

Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240
            L IAEL  +AGLP GV N+V+GDK AVD L+  P V+A SFVGST +AEYIY  GT  G
Sbjct: 181 ALRIAELLQQAGLPDGVFNLVNGDKEAVDTLLNDPRVQAASFVGSTMVAEYIYHTGTAAG 240

Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300
           KRVQALGGAKNHAV+MPDADLDNAV+ALMGAAYGSCGERCMAISV VCVGD +ADA+V  
Sbjct: 241 KRVQALGGAKNHAVVMPDADLDNAVNALMGAAYGSCGERCMAISVVVCVGDTVADAVVGG 300

Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360
           L  ++  LK+G G   G +MGPLVT     KV GY+D G+ +GAELVVDGRG +V GH  
Sbjct: 301 LAEKLAHLKVGPGRESGSEMGPLVTAQHLRKVRGYVDRGLDEGAELVVDGRGQRVEGHAE 360

Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420
           GFFLGG LFDRVTPEM+IY++EIFGPVLC+VRV +L++AM LI++HEYGNGTCIFTRDGE
Sbjct: 361 GFFLGGCLFDRVTPEMSIYRDEIFGPVLCVVRVENLQQAMTLIDNHEYGNGTCIFTRDGE 420

Query: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQR 480
           AAR F D I VGMVGVN+PLPVPVAYHSFGGWKRSLFGDLHAYGPD VRFYT+RK ITQR
Sbjct: 421 AARFFSDHIRVGMVGVNIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTRRKTITQR 480

Query: 481 WPQRKSHEAAQFAFPS 496
           WP     E + +AFP+
Sbjct: 481 WPSASVREGSSYAFPT 496


Lambda     K      H
   0.319    0.137    0.411 

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: 818
Number of extensions: 25
Number of successful extensions: 1
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: 498
Length of database: 497
Length adjustment: 34
Effective length of query: 464
Effective length of database: 463
Effective search space:   214832
Effective search space used:   214832
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 (21.7 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