GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Lutibaculum baratangense AMV1

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_023432895.1 N177_RS13385 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= reanno::Smeli:SMc00781
         (498 letters)



>NCBI__GCF_000496075.1:WP_023432895.1
          Length = 499

 Score =  662 bits (1709), Expect = 0.0
 Identities = 314/496 (63%), Positives = 397/496 (80%)

Query: 3   ELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNP 62
           E+GHFI G+ V G SGR + +++P+TGE  G VALAS+AD+ +AV +A+ A P WAAT P
Sbjct: 4   EIGHFIGGRNVGGGSGRTAPVYDPSTGEEAGRVALASEADVRSAVAAARDAFPDWAATTP 63

Query: 63  QRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQKSE 122
            RRAR+  +F+++L + +++LA +++ EHGKT+ DAKG+I RG+EV EF    P L K E
Sbjct: 64  LRRARILNRFLRILEERIDDLAAVITAEHGKTLSDAKGEIERGMEVVEFATAAPQLLKGE 123

Query: 123 FTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVP 182
            TE  G  ID +S+RQP+G+ AGITPFNFP M+PMWMF  A+ACGN F+LKPSERDPS  
Sbjct: 124 VTENVGTRIDSHSLRQPLGVVAGITPFNFPAMVPMWMFPVALACGNTFVLKPSERDPSAS 183

Query: 183 IRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNGK 242
           I +AE + EAG+P G+ NVV+GDK AVDAILT PD+ AVSFVGSTPIARY+Y TAA  GK
Sbjct: 184 IVIAEWLKEAGVPDGVFNVVHGDKEAVDAILTDPDVQAVSFVGSTPIARYIYETAAKTGK 243

Query: 243 RAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLIDKL 302
           R Q  GGAKNHMI+MPDADLDQAA+AL+GA YGSAGERCMA+SVAVPVGE+TA+ L+ KL
Sbjct: 244 RCQALGGAKNHMIVMPDADLDQAADALMGAAYGSAGERCMAVSVAVPVGEKTADALVAKL 303

Query: 303 VPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYENG 362
            P VE+L++GP TD +++MGP+VTK+   R+ S IDSG+E GA+LVVDGR  KLQGY+NG
Sbjct: 304 KPRVEALKVGPGTDPQSEMGPLVTKQHRDRVLSYIDSGVEAGAELVVDGRGLKLQGYDNG 363

Query: 363 HFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGDA 422
           +++GG LFD VT DM IY+ EIFGPVL V RA ++E A     +HE+GNG AI+TRDGDA
Sbjct: 364 YYVGGTLFDRVTTDMKIYREEIFGPVLCVARAGDFETAAKWINEHEFGNGTAIFTRDGDA 423

Query: 423 ARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITSRW 482
           AR+FA RI +GMVG+NVPIPVP+A+HSFGGWKSS FGD + HG + ++F+TR KTITSRW
Sbjct: 424 AREFAHRIQVGMVGINVPIPVPMAFHSFGGWKSSLFGDHHMHGPEGVRFYTRLKTITSRW 483

Query: 483 PSGIKDGAEFSIPTMR 498
           P+GI+ GA+F +PTMR
Sbjct: 484 PTGIRAGADFVMPTMR 499


Lambda     K      H
   0.319    0.137    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: 785
Number of extensions: 22
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: 499
Length adjustment: 34
Effective length of query: 464
Effective length of database: 465
Effective search space:   215760
Effective search space used:   215760
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 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